Hi. I tired to run MoCaSeq test pipeline several times but every time FILE ERROR happend.

---- Matched BAM-files? ---- Thu Dec 23 12:34:20 UTC 2021 timestamp: 1640262860 +------------+ | FILE ERROR | +------------+ Cannot access BAM file (/var/pipeline/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam). It either does not exist or is not readable.

Could you help me about this problem ?

Hi, please provide us the command you used to call MoCaSeq as well as the full report file located here: MoCaSeq_Test/results/QC/MoCaSeq_Test.report.txt

Additionally the test files are stored with Git LFS, so maybe the download did not work. Could you please check if the files within the test folder are ~50MB?

Thank you for your quick response.

I used this command:

docker run \ -v ${working_directory}:/var/pipeline/ \ rolandradlab/mocaseq:0.4.53 \ --test yes

I attached report file and checked the size of test folder(size is 5,060,317 bytes (5.4 MB on disk) for 152 items).

Thanks

2021年12月23日(木) 22:17 Niklas dAK @.***>:

Hi, please provide us the command you used to call MoCaSeq as well as the full report file located here: MoCaSeq_Test/results/QC/MoCaSeq_Test.report.txt

Additionally the test files are stored with Git LFS, so maybe the download did not work. Could you please check if the files within the test folder are ~50MB?

— Reply to this email directly, view it on GitHub https://github.com/roland-rad-lab/MoCaSeq/issues/8#issuecomment-1000298653, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZ7I75DZVQQ2DCQHZ2S75TUSMOPFANCNFSM5KUX4ZPQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you authored the thread.Message ID: @.***>

---- Checking for available reference files ---- Mon Dec 20 16:03:46 UTC 2021 timestamp: 1640016226 ---- Reference files not found - Files will be downloaded ---- Mon Dec 20 16:03:46 UTC 2021 timestamp: 1640016226 ---- Checking for available reference files ---- Tue Dec 21 05:56:55 UTC 2021 timestamp: 1640066215 ---- Reference files not found - Files will be downloaded ---- Tue Dec 21 05:56:55 UTC 2021 timestamp: 1640066215 ---- Checking for available reference files ---- Tue Dec 21 08:18:52 UTC 2021 timestamp: 1640074732 ---- Reference files not found - Files will be downloaded ---- Tue Dec 21 08:18:52 UTC 2021 timestamp: 1640074732 ---- Starting Mouse Cancer Genome Analysis ---- Starting pipeline using these settings: Wed Dec 22 01:19:57 UTC 2021 timestamp: 1640135997 Running sample named MoCaSeq_Test Running in MS-mode Using /opt/MoCaSeq/test/Mouse.Normal.R1.fastq.gz and /opt/MoCaSeq/test/Mouse.Normal.R2.fastq.gz for normal fastqs Using /opt/MoCaSeq/test/Mouse.Tumor.R1.fastq.gz and /opt/MoCaSeq/test/Mouse.Tumor.R2.fastq.gz for tumor fastqs Assuming that reads are from Mouse Assuming that experiment is WES Reading configuration file from /opt/MoCaSeq/config.sh Setting location of repository to /opt/MoCaSeq/repository Setting location of genome to /var/pipeline/ref/GRCm38.p6 Setting location for temporary files to /var/pipeline/temp Assuming none-artefacts for SNV-calling all is setting for filtering of SNV calls Quality scores are assumed as Using GATK v4.1.7.0 Will run Mutect2 Starting workflow using 4 CPU-threads and 8 GB of RAM ---- Creating directories ---- Wed Dec 22 01:19:57 UTC 2021 timestamp: 1640135997 ---- Copying repository ---- Wed Dec 22 01:19:57 UTC 2021 timestamp: 1640135997 ---- Copying raw data ---- Wed Dec 22 01:19:57 UTC 2021 timestamp: 1640135997 ---- Calculating md5-sums ---- Wed Dec 22 01:19:59 UTC 2021 timestamp: 1640135999 ---- Running FastQC before trimming ---- Wed Dec 22 01:20:00 UTC 2021 timestamp: 1640136000 Started analysis of MoCaSeq_Test.Normal.R1.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R1.fastq.gz Started analysis of MoCaSeq_Test.Normal.R2.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R2.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 25% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 25% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 25% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 25% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 30% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 30% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 30% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 30% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 35% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 35% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 35% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 35% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 40% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 40% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 40% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 40% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 100% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 100% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 100% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 100% complete for MoCaSeq_Test.Tumor.R2.fastq.gz ---- Trimming reads ---- Wed Dec 22 01:20:13 UTC 2021 timestamp: 1640136013 TrimmomaticPE: Started with arguments: -threads 4TrimmomaticPE: Started with arguments: -phred33 MoCaSeq_Test/fastq/MoCaSeq_Test.Normal.R1.fastq.gz -threads 4 MoCaSeq_Test/fastq/MoCaSeq_Test.Normal.R2.fastq.gz -phred33 /var/pipeline/temp/MoCaSeq_Test.Normal.R1.passed.fastq.gz MoCaSeq_Test/fastq/MoCaSeq_Test.Tumor.R1.fastq.gz MoCaSeq_Test/fastq/MoCaSeq_Test.Tumor.R2.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R1.not_passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R1.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R1.not_passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R2.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R2.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R2.not_passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R2.not_passed.fastq.gz LEADING:25 TRAILING:25 LEADING:25 TRAILING:25 MINLEN:50 SLIDINGWINDOW:10:25 MINLEN:50 ILLUMINACLIP:/opt/trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:10:25 ILLUMINACLIP:/opt/trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequencesUsing Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'

Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 1000000 Both Surviving: 972646 (97.26%) Forward Only Surviving: 26622 (2.66%) Reverse Only Surviving: 497 (0.05%) Dropped: 235 (0.02%) TrimmomaticPE: Completed successfully Input Read Pairs: 1000000 Both Surviving: 969667 (96.97%) Forward Only Surviving: 29456 (2.95%) Reverse Only Surviving: 499 (0.05%) Dropped: 378 (0.04%) TrimmomaticPE: Completed successfully ---- Running FastQC after trimming ---- Wed Dec 22 01:21:57 UTC 2021 timestamp: 1640136117 Started analysis of MoCaSeq_Test.Normal.R1.passed.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R1.passed.fastq.gz Started analysis of MoCaSeq_Test.Normal.R2.passed.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 25% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 25% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 25% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 30% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 30% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 30% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 35% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 25% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 35% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 35% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 40% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 30% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 40% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 40% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 35% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 40% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz ---- Removing fastq files ---- Wed Dec 22 01:22:10 UTC 2021 timestamp: 1640136130 ---- Mapping trimmed reads ---- Wed Dec 22 01:22:10 UTC 2021 timestamp: 1640136130 01:22:11.687 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Dec 22 01:22:11 UTC 2021] CleanSam --INPUT /dev/stdin --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.bam --VALIDATION_STRINGENCY LENIENT --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Wed Dec 22 01:22:11 UTC 2021] Executing as @. on Linux 5.10.25-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [bwt_restore_sa] fail to open file '/var/pipeline/ref/GRCm38.p6/bwa_index/GRCm38.p6.sa' : No such file or directory [Wed Dec 22 01:22:19 UTC 2021] picard.sam.CleanSam done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=41418752 01:22:20.850 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Dec 22 01:22:20 UTC 2021] CleanSam --INPUT /dev/stdin --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Normal.cleaned.bam --VALIDATION_STRINGENCY LENIENT --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Wed Dec 22 01:22:20 UTC 2021] Executing as @. on Linux 5.10.25-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [bwt_restore_sa] fail to open file '/var/pipeline/ref/GRCm38.p6/bwa_index/GRCm38.p6.sa' : No such file or directory [Wed Dec 22 01:22:28 UTC 2021] picard.sam.CleanSam done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=41418752 ---- Postprocessing I (Sorting, fixing read groups and marking duplicates) ---- Wed Dec 22 01:22:28 UTC 2021 timestamp: 1640136148

sambamba 0.7.0 by Artem Tarasov and Pjotr Prins (C) 2012-2019 sambamba 0.7.0 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4) LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)

01:22:29.425 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 01:22:29.426 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Dec 22 01:22:29 UTC 2021] AddOrReplaceReadGroups --INPUT /var/pipeline/temp/MoCaSeq_Test.Normal.cleaned.sorted.bam --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Normal.cleaned.sorted.readgroups.bam --RGID 1 --RGLB Lib1 --RGPL ILLUMINA --RGPU Run1 --RGSM Normal --MAX_RECORDS_IN_RAM 2000000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false[Wed Dec 22 01:22:29 UTC 2021] AddOrReplaceReadGroups --INPUT /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.sorted.bam --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.sorted.readgroups.bam --RGID 1 --RGLB Lib1 --RGPL ILLUMINA --RGPU Run1 --RGSM Tumor --MAX_RECORDS_IN_RAM 2000000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false

[Wed Dec 22 01:22:29 UTC 2021] Executing as @. on Linux 5.10.25-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Wed Dec 22 01:22:29 UTC 2021] Executing as @. on Linux 5.10.25-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT INFO 2021-12-22 01:22:29 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=Lib1 SM=Normal

INFO 2021-12-22 01:22:29 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=Lib1 SM=Tumor

[Wed Dec 22 01:22:29 UTC 2021] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=41418752 [Wed Dec 22 01:22:29 UTC 2021] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=41418752

finding positions of the duplicate reads in the file... finding positions of the duplicate reads in the file... /opt/MoCaSeq/MoCaSeq.sh: line 489: 797 Killed /opt/bin/sambamba markdup --tmpdir $temp_dir --t $threads --overflow-list-size=$HASH_TABLE_SIZE --hash-table-size=$HASH_TABLE_SIZE $temp_dir/$name.$type.cleaned.sorted.readgroups.bam $temp_dir/$name.$type.cleaned.sorted.readgroups.marked.bam sorted 0 end pairs and 0 single ends (among them 0 unmatched pairs) collecting indices of duplicate reads... done in 2 ms found 0 duplicates collected list of positions in 0 min 3 sec marking duplicates... collected list of positions in 0 min 3 sec ---- Postprocessing II (Base recalibration) ---- Wed Dec 22 01:22:33 UTC 2021 timestamp: 1640136153 01:22:36.345 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 01:22:36.346 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Dec 22, 2021 1:22:36 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. Dec 22, 2021 1:22:36 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 01:22:36.675 INFO BaseRecalibrator - ------------------------------------------------------------ 01:22:36.675 INFO BaseRecalibrator - ------------------------------------------------------------ 01:22:36.677 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.7.0 01:22:36.677 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.7.0 01:22:36.678 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 01:22:36.678 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 01:22:36.679 INFO BaseRecalibrator - Executing as @. on Linux v5.10.25-linuxkit amd64 01:22:36.679 INFO BaseRecalibrator - Executing as @. on Linux v5.10.25-linuxkit amd64 01:22:36.680 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 01:22:36.680 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 01:22:36.681 INFO BaseRecalibrator - Start Date/Time: December 22, 2021 1:22:36 AM UTC 01:22:36.681 INFO BaseRecalibrator - Start Date/Time: December 22, 2021 1:22:36 AM UTC 01:22:36.681 INFO BaseRecalibrator - ------------------------------------------------------------ 01:22:36.682 INFO BaseRecalibrator - ------------------------------------------------------------ 01:22:36.682 INFO BaseRecalibrator - ------------------------------------------------------------ 01:22:36.683 INFO BaseRecalibrator - ------------------------------------------------------------ 01:22:36.684 INFO BaseRecalibrator - HTSJDK Version: 2.21.2 01:22:36.684 INFO BaseRecalibrator - HTSJDK Version: 2.21.2 01:22:36.684 INFO BaseRecalibrator - Picard Version: 2.21.9 01:22:36.685 INFO BaseRecalibrator - Picard Version: 2.21.9 01:22:36.685 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 01:22:36.686 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 01:22:36.686 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 01:22:36.687 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 01:22:36.688 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 01:22:36.687 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 01:22:36.688 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 01:22:36.689 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 01:22:36.689 INFO BaseRecalibrator - Deflater: IntelDeflater 01:22:36.690 INFO BaseRecalibrator - Deflater: IntelDeflater 01:22:36.690 INFO BaseRecalibrator - Inflater: IntelInflater 01:22:36.690 INFO BaseRecalibrator - Inflater: IntelInflater 01:22:36.691 INFO BaseRecalibrator - GCS max retries/reopens: 20 01:22:36.691 INFO BaseRecalibrator - GCS max retries/reopens: 20 01:22:36.692 INFO BaseRecalibrator - Requester pays: disabled 01:22:36.693 INFO BaseRecalibrator - Requester pays: disabled 01:22:36.693 INFO BaseRecalibrator - Initializing engine 01:22:36.693 INFO BaseRecalibrator - Initializing engine 01:22:36.819 INFO BaseRecalibrator - Shutting down engine [December 22, 2021 1:22:36 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=141033472

A USER ERROR has occurred: Couldn't read file. Error was: /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.sorted.readgroups.marked.bam with exception: Cannot read non-existent file: file:///var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.sorted.readgroups.marked.bam

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. 01:22:37.067 INFO FeatureManager - Using codec VCFCodec to read file file:///var/pipeline/ref/GRCm38.p6/MGP.v5.snp_and_indels.exclude_wild.vcf.gz 01:22:37.163 INFO BaseRecalibrator - Shutting down engine [December 22, 2021 1:22:37 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=188743680

A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found. reference contigs = [1, GL456210.1, GL456211.1, GL456212.1, GL456213.1, GL456221.1, 2, 3, 4, GL456216.1, JH584292.1, GL456350.1, JH584293.1, JH584294.1, JH584295.1, 5, JH584296.1, JH584297.1, JH584298.1, GL456354.1, JH584299.1, 6, 7, GL456219.1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, GL456233.1, Y, JH584300.1, JH584301.1, JH584302.1, JH584303.1, GL456239.1, GL456367.1, GL456378.1, GL456381.1, GL456382.1, GL456383.1, GL456385.1, GL456390.1, GL456392.1, GL456393.1, GL456394.1, GL456359.1, GL456360.1, GL456396.1, GL456372.1, GL456387.1, GL456389.1, GL456370.1, GL456379.1, GL456366.1, GL456368.1, JH584304.1, KV575234.1, KK082441.1, KV575232.1, KV575233.1, KV575235.1, KV575236.1, KQ030484.1, KZ289066.1, KZ289065.1, KZ289064.1, KQ030485.1, KQ030486.1, KZ289070.1, KZ289067.1, KQ030487.1, KQ030488.1, KQ030489.1, KZ289069.1, JH792826.1, KZ289068.1, JH792827.1, KV575237.1, KK082443.1, KK082442.1, JH792828.1, KV575238.1, KV575239.1, KV575240.1, KQ030490.1, KB469738.3, KZ289071.1, KQ030491.1, KZ289072.1, KZ289076.1, KZ289073.1, KZ289077.1, KZ289080.1, KZ289078.1, KZ289074.1, KZ289081.1, KZ289079.1, KZ289075.1, KB469739.1, KB469740.1, KZ289082.1, KZ289083.1, KZ289084.1, KQ030492.1, KV575241.1, KQ030493.2, KZ289086.1, KZ289085.1, KB469741.2, KZ289087.1, KZ289088.1, KZ289089.1, KB469742.1, JH792829.1, KZ289090.1, KZ289091.1, JH792830.1, KQ030494.1, KV575242.1, KZ289093.1, KQ030496.1, KQ030497.1, JH792831.2, KZ289094.1, KQ030495.1, KZ289095.1, KZ289092.1, JH792832.1, JH792834.1, JH792833.1, GL456079.1, GL456024.2, GL456007.1, GL456006.1, GL456008.1, GL456011.1, GL456025.1, GL456026.2, GL456014.1, GL456074.1, GL456017.2, JH584305.1, GL456019.1, JH584306.1, JH584307.1, JH590470.1, JH584308.1, JH584309.1, GL456032.1, GL456033.2, GL456031.1, GL456013.1, GL455993.1, GL455991.1, GL455992.2, GL455994.1, GL455995.1, GL455996.1, GL455997.1, GL455998.1, GL455999.2, GL456000.1, JH584310.1, JH584311.1, JH584312.1, GL456001.2, JH584313.1, JH584314.1, GL456021.2, GL456002.2, GL456003.2, GL456004.1, JH584315.1, GL456005.1, GL456010.1, GL456012.2, GL456065.1, GL456016.1, GL456020.1, GL456028.2, GL456022.2, GL455990.1, GL456080.1, GL456081.1, GL456082.1, GL455989.1, GL456068.1, JH584316.1, JH584317.1, JH584318.1, GL456071.1, GL456072.1, GL456073.1, JH584320.1, JH584321.1, JH584322.1, GL456048.1, GL456045.2, GL456049.2, JH584323.1, GL456044.2, GL456042.2, JH584324.1, JH584325.1, GL456053.2, JH584326.1, JH584327.1, GL456060.2, JH584328.1, GL456050.1, JH584264.1, GL456054.2, JH584265.1, JH584267.1, JH584266.1, GL456349.1, GL456070.1, GL456064.1, GL456009.1, GL456015.1, GL456069.1, JH584319.1, JH584269.1, JH584268.1, GL456077.1, GL456075.1, GL456076.1, GL456078.1, JH584270.1, AY172335.1] reads contigs = []

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Quality control I (Sequencing artifacts, multiple metrics) ---- Wed Dec 22 01:22:37 UTC 2021 timestamp: 1640136157 [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory[E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory

samtools idxstats: failed to open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam"samtools idxstats: failed to open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory : No such file or directory 01:22:38.191 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Dec 22 01:22:38 UTC 2021] CollectMultipleMetrics --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Tumor.bam.metrics --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --ASSUME_SORTED true --STOP_AFTER 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectBaseDistributionByCycle --PROGRAM CollectInsertSizeMetrics --PROGRAM MeanQualityByCycle --PROGRAM QualityScoreDistribution --INCLUDE_UNPAIRED false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Wed Dec 22 01:22:38 UTC 2021] Executing as @.*** on Linux 5.10.25-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Wed Dec 22 01:22:38 UTC 2021] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=41418752 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///var/pipeline/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392)01:22:38.273 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:95)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:563)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

issues If possible, please include a log file that triggers the error - the last file found was: None

Module somalier raised an exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/multiqc/multiqc.py", line 567, in run mod = config.avail_modules[this_module].load() File "/usr/local/lib/python2.7/dist-packages/pkg_resources/init.py", line 2443, in load return self.resolve() File "/usr/local/lib/python2.7/dist-packages/pkg_resources/init.py", line 2449, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/usr/local/lib/python2.7/dist-packages/multiqc/modules/somalier/init.py", line 3, in from .somalier import MultiqcModule File "/usr/local/lib/python2.7/dist-packages/multiqc/modules/somalier/somalier.py", line 698 cols_return.append('rgba({},{},{},{})'.format(cols_rgb, alpha)) SyntaxError: only named arguments may follow expression

[INFO ] fastqc : Found 8 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : MoCaSeq_Test/results/QC/MoCaSeq_Test.html [INFO ] multiqc : Data : MoCaSeq_Test/results/QC/MoCaSeq_Test_data pandoc: unrecognized option --pdf-engine=xelatex' Try pandoc --help for more information. [ERROR ] multiqc : Error creating PDF! Pandoc returned a non-zero exit code. [INFO ] multiqc : MultiQC complete ---- Matched BAM-files? ---- Wed Dec 22 01:22:50 UTC 2021 timestamp: 1640136170 ---- Get genotypes ---- Wed Dec 22 01:22:50 UTC 2021 timestamp: 1640136170 [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiontis functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup optionvis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optionuis functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup optiont` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam"[E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory: No such file or directory

samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory[E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory samtools depth: samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools depth: [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directoryCould not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" samtools depth: : No such file or directory Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory[E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory

samtools depth: samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam"Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory : No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory rm: cannot remove 'Rplots.pdf': No such file or directory ---- Running Manta (matched tumor-normal) ---- Wed Dec 22 01:22:54 UTC 2021 timestamp: 1640136174 Usage: configManta.py [options]

configManta.py: error: Can't find normal sample BAM/CRAM file: '/var/pipeline/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam' python2: can't open file 'MoCaSeq_Test/results/Manta/runWorkflow.py': [Errno 2] No such file or directory cp: cannot stat 'MoCaSeq_Test/results/Manta/results/variants/somaticSV.vcf.gz': No such file or directory gzip: MoCaSeq_Test/results/Manta/MoCaSeq_Test.man.vcf.gz: No such file or directory cat: MoCaSeq_Test/results/Manta/MoCaSeq_Test.man.vcf: No such file or directory Failed to read from MoCaSeq_Test/results/Manta/MoCaSeq_Test.Manta.vcf.gz: unknown file type rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.man.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.one.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.vcf.gz.tbi': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.one.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.vcf.gz.tbi': No such file or directory rm: cannot remove 'Mutect2FilteringStats.tsv': No such file or directory

-------------------- EXCEPTION -------------------- MSG: ERROR: PolyPhen not available

STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::check_sift_polyphen /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:168 STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:121 STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:150 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:121 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Wed Dec 22 01:23:16 2021 Ensembl API version = 96

STATUS: Running VEP and writing to: MoCaSeq_Test/results/Manta/MoCaSeq_Test.Manta.vep.vcf ---- Running Strelka (matched tumor-normal) ---- Wed Dec 22 01:23:46 UTC 2021 timestamp: 1640136226 Usage: configureStrelkaSomaticWorkflow.py [options]

configureStrelkaSomaticWorkflow.py: error: Can't find expected candidate indel vcf file: 'MoCaSeq_Test/results/Manta/results/variants/candidateSmallIndels.vcf.gz' python2: can't open file 'MoCaSeq_Test/results/Strelka/Strelka/runWorkflow.py': [Errno 2] No such file or directory ---- Strelka Postprocessing I (Indel size selection, filtering) ---- Wed Dec 22 01:23:46 UTC 2021 timestamp: 1640136226 gzip: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.snvs.vcf.gz: No such file or directory gzip: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.indels.vcf.gz: No such file or directory cat: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.snvs.vcf: No such file or directory cat: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.indels.vcf: No such file or directory 01:23:48.270 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Dec 22, 2021 1:23:48 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 01:23:48.452 INFO SelectVariants - ------------------------------------------------------------ 01:23:48.453 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.1.7.0 01:23:48.454 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 01:23:48.455 INFO SelectVariants - Executing as @.*** on Linux v5.10.25-linuxkit amd64 01:23:48.455 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 01:23:48.456 INFO SelectVariants - Start Date/Time: December 22, 2021 1:23:48 AM UTC 01:23:48.456 INFO SelectVariants - ------------------------------------------------------------ 01:23:48.457 INFO SelectVariants - ------------------------------------------------------------ 01:23:48.458 INFO SelectVariants - HTSJDK Version: 2.21.2 01:23:48.458 INFO SelectVariants - Picard Version: 2.21.9 01:23:48.459 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 01:23:48.459 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 01:23:48.460 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 01:23:48.460 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 01:23:48.461 INFO SelectVariants - Deflater: IntelDeflater 01:23:48.461 INFO SelectVariants - Inflater: IntelInflater 01:23:48.462 INFO SelectVariants - GCS max retries/reopens: 20 01:23:48.462 INFO SelectVariants - Requester pays: disabled 01:23:48.463 INFO SelectVariants - Initializing engine 01:23:48.678 INFO SelectVariants - Shutting down engine [December 22, 2021 1:23:48 AM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=178782208

A USER ERROR has occurred: Cannot read file:///var/pipeline/MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.filtered.vcf because no suitable codecs found

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Strelka Postprocessing II (Filtering out known SNV/Indel using dbSNP or the Sanger Mouse database) ---- Wed Dec 22 01:23:48 UTC 2021 timestamp: 1640136228 [bgzip] No such file or directory: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf tbx_index_build failed: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz" : No such file or directory Failed to open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz: No such file or directory Failed to open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.snp.postprocessed.vcf.gz: unknown file type mv: cannot stat 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.snp.postprocessed.snp_removed.vcf.gz'mv: cannot stat 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.snp_removed.vcf.gz': No such file or directory : No such file or directory gzip: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vcf.gz: No such file or directory gzip: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vcf.gz: No such file or directory ---- Strelka Postprocessing III (Extracting allele frequencies) ---- Wed Dec 22 01:23:48 UTC 2021 timestamp: 1640136228

-------------------- EXCEPTION -------------------- MSG: ERROR: Cache directory /var/.vep/mus_musculus not found

STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311 STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Wed Dec 22 01:23:49 2021 Ensembl API version = 96

-------------------- EXCEPTION -------------------- MSG: ERROR: Cache directory /var/.vep/mus_musculus not found

STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311 STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEM

So the issue here is, that the reference files are not downloaded as they should be (your ref/ folder is probably empty).

Let's try to fix this: First enter the docker ennvironment using this:

docker run \
-it --entrypoint=/bin/bash \
-v ${working_directory}:/var/pipeline/ \
rolandradlab/mocaseq:0.4.53

You are now inside the docker container with all the tools installed and code available.

Now executing the following lines:

rm -r temp/ ref/
mkdir temp/
Preparation_GetReferenceDataMouse.sh config-file-from-git-folder temp/ 2>&1 | tee GetReferenceLog.txt

This should start the download and indexing of the needed reference files (this takes a while). This is working for me right now, but sent me the log file in case something goes wrong.

After that can exit the container using the "exit" command, move the reference files somewhere save and always mount it like this:

docker run \ -v ${working_directory}:/var/pipeline/ \ -v ${ref_directory}:/var/pipeline/ref/ rolandradlab/mocaseq:0.4.53 \ --test yes

Hope this helps.

I tried as you mentioned but it seemed the reference was not created correctly... I attached GetReferenceData.txt & GetReferenceLog.txt.

2021年12月27日(月) 17:31 Niklas dAK @.***>:

So the issue here is, that the reference files are not downloaded as they should be (your ref/ folder is probably empty).

Let's try to fix this: First enter the docker ennvironment using this:

docker run \ -it --entrypoint=/bin/bash \ -v ${working_directory}:/var/pipeline/ \ rolandradlab/mocaseq:0.4.53

You are now inside the docker container with all the tools installed and code available.

Now executing the following lines:

rm -r temp/ ref/ mkdir temp/ Preparation_GetReferenceDataMouse.sh config-file-from-git-folder temp/ 2>&1 | tee GetReferenceLog.txt

This should start the download and indexing of the needed reference files (this takes a while). This is working for me right now, but sent me the log file in case something goes wrong.

After that can exit the container using the "exit" command, move the reference files somewhere save and always mount it like this:

docker run -v ${working_directory}:/var/pipeline/ -v ${ref_directory}:/var/pipeline/ref/ rolandradlab/mocaseq:0.4.53 --test yes

Hope this helps.

— Reply to this email directly, view it on GitHub https://github.com/roland-rad-lab/MoCaSeq/issues/8#issuecomment-1001431813, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZ7I764OM3PO2J3HWCUWXDUTAP7XANCNFSM5KUX4ZPQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you authored the thread.Message ID: @.***>

---- Get reference data ---- ---- Generate reference data for Version GRCm38.p6 ---- Thu Dec 30 13:54:56 UTC 2021 ---- Copying over files from repository ---- Thu Dec 30 13:54:56 UTC 2021 ---- Downloading reference genome ---- Thu Dec 30 13:54:56 UTC 2021 2021-12-30 14:01:24 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz [864826863] -> "ref/GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz" [1]

gzip: ref/GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz: invalid compressed data--format violated mv: cannot stat 'ref/GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna': No such file or directory ---- Generate BWA Index ---- Thu Dec 30 14:01:34 UTC 2021 sed: can't read ref/GRCm38.p6/GRCm38.p6.fna: No such file or directory [E::fai_build3_core] Failed to open the file ref/GRCm38.p6/GRCm38.p6.fna [faidx] Could not build fai index ref/GRCm38.p6/GRCm38.p6.fna.fai grep: ref/GRCm38.p6/GRCm38.p6.fna: No such file or directory [E::fai_build3_core] Failed to open the file ref/GRCm38.p6/GRCm38.p6.fna [faidx] Could not build fai index ref/GRCm38.p6/GRCm38.p6.fna.fai grep: ref/GRCm38.p6/GRCm38.p6.fna: No such file or directory [E::fai_build3_core] Failed to open the file ref/GRCm38.p6/GRCm38.p6.fna [faidx] Could not build fai index ref/GRCm38.p6/GRCm38.p6.fna.fai [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... Floating point exception [E::bwa_idx_load_from_disk] fail to locate the index files samtools sort: failed to read header from "ref/GRCm38.p6/alt_mapping_unsorted.sam" [E::hts_open_format] Failed to open file "ref/GRCm38.p6/alt_mapping_nosup.sam" : No such file or directory samtools view: failed to open "ref/GRCm38.p6/alt_mapping_nosup.sam" for reading: No such file or directory grep: ref/GRCm38.p6/alt_mapping.sam: No such file or directory grep: ref/GRCm38.p6/alt_mapping.sam: No such file or directory grep: ref/GRCm38.p6/alt_mapping.sam: No such file or directory [bwa_idx_build] fail to open file 'ref/GRCm38.p6/GRCm38.p6.fna' : No such file or directory rm: cannot remove 'ref/GRCm38.p6/alt_mapping.sam': No such file or directory rm: cannot remove 'ref/GRCm38.p6/alt_mapping_nosup.sam': No such file or directory ---- Generate sequence dictionary ---- Thu Dec 30 14:01:34 UTC 2021 14:01:35.313 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Dec 30 14:01:35 UTC 2021] CreateSequenceDictionary --OUTPUT ref/GRCm38.p6/GRCm38.p6.dict --REFERENCE ref/GRCm38.p6/GRCm38.p6.fna --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Dec 30 14:01:35 UTC 2021] Executing as @. on Linux 5.10.76-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Thu Dec 30 14:01:35 UTC 2021] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=41418752 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: ref/GRCm38.p6/GRCm38.p6.fna at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:609) at htsjdk.samtools.reference.FastaSequenceFile.(FastaSequenceFile.java:64) at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:143) at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:99) at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:87) at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:215) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) Caused by: java.nio.file.NoSuchFileException: ref/GRCm38.p6/GRCm38.p6.fna at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86) at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107) at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214) at java.nio.file.Files.newByteChannel(Files.java:361) at java.nio.file.Files.newByteChannel(Files.java:407) at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384) at java.nio.file.Files.newInputStream(Files.java:152) at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:605) ... 8 more ---- Generate exons covered by SureSelect ---- Thu Dec 30 14:01:35 UTC 2021 14:01:36.257 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Dec 30 14:01:36 UTC 2021] BedToIntervalList --INPUT ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed --SEQUENCE_DICTIONARY ref/GRCm38.p6/GRCm38.p6.dict --OUTPUT ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --SORT true --UNIQUE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Dec 30 14:01:36 UTC 2021] Executing as @. on Linux 5.10.76-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Thu Dec 30 14:01:36 UTC 2021] picard.util.BedToIntervalList done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=41418752 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" picard.PicardException: Sequence '1' was not found in the sequence dictionary at picard.util.BedToIntervalList.doWork(BedToIntervalList.java:144) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) ---- Downloading reference genome (for VEP) ---- Thu Dec 30 14:01:36 UTC 2021 2021-12-30 14:11:06 URL: ftp://ftp.ensembl.org/pub/release-96/variation/indexed_vep_cache/mus_musculus_vep_96_GRCm38.tar.gz [1463782096] -> "ref/GRCm38.p6/VEP/mus_musculus_vep_96_GRCm38.tar.gz" [1] ---- Generate customized Sanger DB ---- Thu Dec 30 14:13:58 UTC 2021 2021-12-30 14:14:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/ [29276] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/.listing" [1] 2021-12-30 14:14:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz [55622330] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:14:19 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:14:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [982936] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:14:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [88] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:15:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz [235966892] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:15:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:15:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1149443] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:16:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:16:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [58575661] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:16:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:16:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1031914] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:16:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [87] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:18:22 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz [211532192] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:18:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:18:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1189688] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:18:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:19:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz [42189852] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:19:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:19:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [893761] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:19:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [88] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:20:13 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz [216725846] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:20:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:20:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1149402] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:20:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:20:53 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [57351895] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:20:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:21:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1046489] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:21:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:22:05 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz [200078623] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:22:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [65] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:22:13 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1192350] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:22:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:22:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [57664949] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:22:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:22:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1047038] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:22:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:23:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz [203371139] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:23:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:24:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1208820] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:24:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:24:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [53342191] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:24:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:24:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1008737] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:24:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:25:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz [186363860] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:25:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:25:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1147448] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:25:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:26:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [53890220] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:26:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [89] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:26:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1007726] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:26:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [93] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:27:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz [173804988] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:27:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:27:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1094144] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:27:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:28:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [56916808] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:28:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:28:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1042711] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:28:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:29:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz [208769733] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:29:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:29:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1196235] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:29:45 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:30:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz [46250554] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:30:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:30:22 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [994308] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:30:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:31:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz [175300582] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:31:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:31:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1123517] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:31:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:32:05 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [58710483] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:32:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:32:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1043079] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:32:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:33:05 (3.88 MB/s) - Control connection closed. 2021-12-30 14:48:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz [204244588] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:48:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:48:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1175979] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:48:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:48:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz [5929999] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:48:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:48:46 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [346568] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:48:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:48:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz [17321974] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:48:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:49:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [369781] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:49:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:49:05 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [1670145] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:49:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:49:09 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [243771] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:49:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:49:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz [7164392] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:49:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:49:35 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [491689] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:49:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:49:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [28977350] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:49:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:50:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [679229] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:50:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:50:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz [106537762] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:50:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:50:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [746658] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:50:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:51:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [28705588] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:51:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:51:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [690724] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:51:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:51:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz [105062300] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:51:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:52:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [743194] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:52:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:52:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [33969296] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:52:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:52:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [763820] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:52:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 14:53:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz [113621435] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 14:53:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 14:53:16 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [790208] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 14:53:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 14:54:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [175277822] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 14:54:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [80] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 14:54:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1498042] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 14:54:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 16:47:27 (75.7 KB/s) - Data connection: Connection timed out; Control connection closed. 2021-12-30 17:03:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz [785849127] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz" [2] 2021-12-30 17:03:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [70] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:03:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1870634] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:03:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:04:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [59765930] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:04:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:04:35 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1058279] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:04:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:05:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz [207660687] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:05:41 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:05:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1180402] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:05:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:06:25 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz [58038828] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:06:26 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:06:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1035459] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:06:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:07:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz [202228594] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:07:53 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:07:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1115834] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:07:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:08:45 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz [58439864] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:08:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:08:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1033073] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:08:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:09:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz [207469504] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:09:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:10:05 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1169915] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:10:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:10:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [55091563] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:10:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:10:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1022214] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:10:41 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:11:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz [206335215] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:11:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:11:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1162437] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:11:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:12:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [61167754] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:12:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:12:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1062370] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:12:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:13:26 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz [216418425] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:13:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:13:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1206806] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:13:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:14:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [63953918] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:14:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:14:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1065205] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:14:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:15:20 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz [226946659] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:15:21 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:15:26 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1160649] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:15:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:16:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [71234620] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:16:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:16:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1360230] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:16:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:17:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz [245949406] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:17:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:17:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1504105] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:17:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LEWES_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:17:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [60805022] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:17:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [76] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:17:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1053551] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2021-12-30 17:17:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [80] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2021-12-30 17:18:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz [216017686] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2021-12-30 17:18:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [66] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2021-12-30 17:18:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1191135] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2021-12-30 17:18:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [70] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/LP_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2021-12-30 17:20:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/MOLF_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [160452053] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/MOLF_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2021-12-30 17:20:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/MOLF_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [80] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/MOLF_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2021-12-30 17:20:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/MOLF_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1456900] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/MOLF_EiJ.mgp.v5

Looks like the download of the FASTA file is not working for some reason, maybe permission or unstable connection issues?

Try the following individual commands from the script: wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz

There should be a 860,9 MB .gz file now and then 2.9 GB after decompressing.

gunzip GCA_000001635.8_GRCm38.p6_genomic.fna.gz

Hi, I tried again. This time it succeeded in downloading and decompressing 2.85GB of "GRCm38.p6.fna" but it seems there still be some problem with generating reference files(I tried several times before and this problem is maybe the same problem). I attached "GetReferenceData.txt" Please help me with this problem.

2022年1月4日(火) 17:53 Niklas dAK @.***>:

Looks like the download of the FASTA file is not working for some reason, maybe permission or unstable connection issues?

Try the following individual commands from the script: wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz

There should be a 860,9 MB .gz file now and then 2.9 GB after decompressing.

gunzip GCA_000001635.8_GRCm38.p6_genomic.fna.gz

— Reply to this email directly, view it on GitHub https://github.com/roland-rad-lab/MoCaSeq/issues/8#issuecomment-1004626510, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZ7I7ZZENPIX2ZOKB3SBXLUUKYP5ANCNFSM5KUX4ZPQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you authored the thread.Message ID: @.***>

Sorry again. I forgot to attach the file.

Thanks.

2022年1月6日(木) 10:18 Takahiro Matsunaga @.***>:

Hi, I tried again. This time it succeeded in downloading and decompressing 2.85GB of "GRCm38.p6.fna" but it seems there still be some problem with generating reference files(I tried several times before and this problem is maybe the same problem). I attached "GetReferenceData.txt" Please help me with this problem.

2022年1月4日(火) 17:53 Niklas dAK @.***>:

Looks like the download of the FASTA file is not working for some reason, maybe permission or unstable connection issues?

Try the following individual commands from the script: wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz

There should be a 860,9 MB .gz file now and then 2.9 GB after decompressing.

gunzip GCA_000001635.8_GRCm38.p6_genomic.fna.gz

— Reply to this email directly, view it on GitHub https://github.com/roland-rad-lab/MoCaSeq/issues/8#issuecomment-1004626510, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZ7I7ZZENPIX2ZOKB3SBXLUUKYP5ANCNFSM5KUX4ZPQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you authored the thread.Message ID: @.***>

---- Get reference data ---- ---- Generate reference data for Version GRCm38.p6 ---- Tue Jan 4 09:46:54 UTC 2022 ---- Copying over files from repository ---- Tue Jan 4 09:46:54 UTC 2022 ---- Downloading reference genome ---- Tue Jan 4 09:46:55 UTC 2022 2022-01-04 09:53:52 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz [860916719] -> "ref/GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz" [1] ---- Generate BWA Index ---- Tue Jan 4 09:55:20 UTC 2022 [bwa_index] Pack FASTA... 18.42 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=5451042740, availableWord=395555492 [BWTIncConstructFromPacked] 10 iterations done. 99999988 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999988 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999988 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999988 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999988 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999988 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999988 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999988 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999988 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999988 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999988 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999988 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999988 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999988 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999988 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999988 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999988 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999988 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999988 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999988 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099999988 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2199999988 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2299999988 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2399999988 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2499999988 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2599999988 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2699999988 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2799999988 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2899999988 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2999999988 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 3099999988 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 3199999988 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 3299999988 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 3399999988 characters processed. [BWTIncConstructFromPacked] 350 iterations done. 3499999988 characters processed. [BWTIncConstructFromPacked] 360 iterations done. 3599999988 characters processed. [BWTIncConstructFromPacked] 370 iterations done. 3699999988 characters processed. [BWTIncConstructFromPacked] 380 iterations done. 3799999988 characters processed. [BWTIncConstructFromPacked] 390 iterations done. 3899999988 characters processed. [BWTIncConstructFromPacked] 400 iterations done. 3999999988 characters processed. [BWTIncConstructFromPacked] 410 iterations done. 4099999988 characters processed. [BWTIncConstructFromPacked] 420 iterations done. 4199999988 characters processed. [BWTIncConstructFromPacked] 430 iterations done. 4299999988 characters processed. [BWTIncConstructFromPacked] 440 iterations done. 4399999988 characters processed. [BWTIncConstructFromPacked] 450 iterations done. 4499999988 characters processed. [BWTIncConstructFromPacked] 460 iterations done. 4599999988 characters processed. [BWTIncConstructFromPacked] 470 iterations done. 4699999988 characters processed. [BWTIncConstructFromPacked] 480 iterations done. 4799663908 characters processed. [BWTIncConstructFromPacked] 490 iterations done. 4891318228 characters processed. [BWTIncConstructFromPacked] 500 iterations done. 4972776836 characters processed. [BWTIncConstructFromPacked] 510 iterations done. 5045173444 characters processed. [BWTIncConstructFromPacked] 520 iterations done. 5109515732 characters processed. [BWTIncConstructFromPacked] 530 iterations done. 5166699284 characters processed. [BWTIncConstructFromPacked] 540 iterations done. 5217520164 characters processed. [BWTIncConstructFromPacked] 550 iterations done. 5262685908 characters processed. [BWTIncConstructFromPacked] 560 iterations done. 5302825316 characters processed. [BWTIncConstructFromPacked] 570 iterations done. 5338497268 characters processed. [BWTIncConstructFromPacked] 580 iterations done. 5370198564 characters processed. [BWTIncConstructFromPacked] 590 iterations done. 5398370724 characters processed. [BWTIncConstructFromPacked] 600 iterations done. 5423406180 characters processed. [BWTIncConstructFromPacked] 610 iterations done. 5445653684 characters processed. [bwt_gen] Finished constructing BWT in 613 iterations. [bwa_index] 2752.80 seconds elapse. [bwa_index] Update BWT... Killed [bwt_restore_sa] fail to open file 'ref/GRCm38.p6/primary_index/bwa_index.sa' : No such file or directory samtools sort: failed to read header from "ref/GRCm38.p6/alt_mapping_unsorted.sam" [E::hts_open_format] Failed to open file "ref/GRCm38.p6/alt_mapping_nosup.sam" : No such file or directory samtools view: failed to open "ref/GRCm38.p6/alt_mapping_nosup.sam" for reading: No such file or directory grep: ref/GRCm38.p6/alt_mapping.sam: No such file or directory grep: ref/GRCm38.p6/alt_mapping.sam: No such file or directory grep: ref/GRCm38.p6/alt_mapping.sam: No such file or directory [bwa_index] Pack FASTA... 18.87 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=5637949096, availableWord=408706560 [BWTIncConstructFromPacked] 10 iterations done. 99999992 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999992 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999992 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999992 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999992 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999992 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999992 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999992 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999992 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999992 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999992 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999992 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999992 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999992 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999992 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999992 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999992 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999992 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999992 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999992 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099999992 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2199999992 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2299999992 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2399999992 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2499999992 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2599999992 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2699999992 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2799999992 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2899999992 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2999999992 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 3099999992 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 3199999992 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 3299999992 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 3399999992 characters processed. [BWTIncConstructFromPacked] 350 iterations done. 3499999992 characters processed. [BWTIncConstructFromPacked] 360 iterations done. 3599999992 characters processed. [BWTIncConstructFromPacked] 370 iterations done. 3699999992 characters processed. [BWTIncConstructFromPacked] 380 iterations done. 3799999992 characters processed. [BWTIncConstructFromPacked] 390 iterations done. 3899999992 characters processed. [BWTIncConstructFromPacked] 400 iterations done. 3999999992 characters processed. [BWTIncConstructFromPacked] 410 iterations done. 4099999992 characters processed. [BWTIncConstructFromPacked] 420 iterations done. 4199999992 characters processed. [BWTIncConstructFromPacked] 430 iterations done. 4299999992 characters processed. [BWTIncConstructFromPacked] 440 iterations done. 4399999992 characters processed. [BWTIncConstructFromPacked] 450 iterations done. 4499999992 characters processed. [BWTIncConstructFromPacked] 460 iterations done. 4599999992 characters processed. [BWTIncConstructFromPacked] 470 iterations done. 4699999992 characters processed. [BWTIncConstructFromPacked] 480 iterations done. 4799999992 characters processed. [BWTIncConstructFromPacked] 490 iterations done. 4899999992 characters processed. [BWTIncConstructFromPacked] 500 iterations done. 4999190584 characters processed. [BWTIncConstructFromPacked] 510 iterations done. 5089448040 characters processed. [BWTIncConstructFromPacked] 520 iterations done. 5169665112 characters processed. [BWTIncConstructFromPacked] 530 iterations done. 5240958232 characters processed. [BWTIncConstructFromPacked] 540 iterations done. 5304319720 characters processed. [BWTIncConstructFromPacked] 550 iterations done. 5360631560 characters processed. [BWTIncConstructFromPacked] 560 iterations done. 5410677672 characters processed. [BWTIncConstructFromPacked] 570 iterations done. 5455154744 characters processed. [BWTIncConstructFromPacked] 580 iterations done. 5494682040 characters processed. [BWTIncConstructFromPacked] 590 iterations done. 5529809992 characters processed. [BWTIncConstructFromPacked] 600 iterations done. 5561027784 characters processed. [BWTIncConstructFromPacked] 610 iterations done. 5588770200 characters processed. [BWTIncConstructFromPacked] 620 iterations done. 5613423720 characters processed. [BWTIncConstructFromPacked] 630 iterations done. 5635331768 characters processed. [bwt_gen] Finished constructing BWT in 632 iterations. [bwa_index] 2866.39 seconds elapse. [bwa_index] Update BWT... Killed rm: cannot remove 'ref/GRCm38.p6/alt_mapping.sam': No such file or directory rm: cannot remove 'ref/GRCm38.p6/alt_mapping_nosup.sam': No such file or directory ---- Generate sequence dictionary ---- Tue Jan 4 17:53:23 UTC 2022 17:53:25.722 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Jan 04 17:53:25 UTC 2022] CreateSequenceDictionary --OUTPUT ref/GRCm38.p6/GRCm38.p6.dict --REFERENCE ref/GRCm38.p6/GRCm38.p6.fna --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Tue Jan 04 17:53:25 UTC 2022] Executing as @. on Linux 5.10.76-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Tue Jan 04 17:53:56 UTC 2022] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.52 minutes. Runtime.totalMemory()=517472256 ---- Generate exons covered by SureSelect ---- Tue Jan 4 17:53:56 UTC 2022 17:53:59.053 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Jan 04 17:53:59 UTC 2022] BedToIntervalList --INPUT ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed --SEQUENCE_DICTIONARY ref/GRCm38.p6/GRCm38.p6.dict --OUTPUT ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --SORT true --UNIQUE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Tue Jan 04 17:53:59 UTC 2022] Executing as @. on Linux 5.10.76-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Tue Jan 04 17:54:07 UTC 2022] picard.util.BedToIntervalList done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=232259584 ---- Downloading reference genome (for VEP) ---- Tue Jan 4 17:54:07 UTC 2022 2022-01-04 18:01:53 URL: ftp://ftp.ensembl.org/pub/release-96/variation/indexed_vep_cache/mus_musculus_vep_96_GRCm38.tar.gz [1463782096] -> "ref/GRCm38.p6/VEP/mus_musculus_vep_96_GRCm38.tar.gz" [1] ---- Generate customized Sanger DB ---- Tue Jan 4 18:05:50 UTC 2022 2022-01-04 18:05:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/ [29276] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/.listing" [1] 2022-01-04 18:06:13 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz [55622330] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:06:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:06:16 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [982936] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:06:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [88] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:07:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz [235966892] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:07:41 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:07:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1149443] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:07:44 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:08:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [58575661] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:08:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:08:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1031914] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:08:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [87] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:09:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz [211532192] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:09:16 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:09:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1189688] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:09:19 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:09:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz [42189852] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:09:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:09:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [893761] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:09:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [88] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:10:46 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz [216725846] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:10:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:10:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1149402] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:10:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:11:09 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [57351895] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:11:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:11:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1046489] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:11:13 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:12:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz [200078623] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:12:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [65] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:12:19 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1192350] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:12:20 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:12:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [57664949] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:12:41 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:12:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1047038] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:12:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:13:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz [203371139] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:13:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:13:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1208820] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:13:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:14:10 (2.95 MB/s) - Control connection closed. 2022-01-04 18:29:09 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [53342191] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:29:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:29:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1008737] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:29:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:30:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz [186363860] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:30:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:30:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1147448] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:30:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:30:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [53890220] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:30:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [89] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:30:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1007726] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:30:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [93] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:31:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz [173804988] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:31:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:31:41 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1094144] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:31:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:32:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [56916808] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:32:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:32:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1042711] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:32:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:33:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz [208769733] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:33:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:33:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1196235] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:33:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:33:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz [46250554] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:33:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:33:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [994308] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:33:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:34:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz [175300582] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:34:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:34:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1123517] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:34:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:34:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [58710483] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:34:53 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:34:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1043079] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:34:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:36:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz [204244588] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:36:25 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:36:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1175979] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:36:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:36:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz [5929999] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:36:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:36:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [346568] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:36:35 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:36:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz [17321974] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:36:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:36:44 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [369781] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:36:45 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:36:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [1670145] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:36:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:36:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [243771] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:36:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:37:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz [7164392] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:37:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:37:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [491689] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:37:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:37:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [28977350] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:37:16 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:37:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [679229] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:37:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:37:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz [106537762] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:38:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:38:02 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [746658] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:38:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:38:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [28705588] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:38:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:38:16 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [690724] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:38:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:38:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz [105062300] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:38:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:38:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [743194] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:38:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:39:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [33969296] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:39:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:39:09 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [763820] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:39:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:39:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz [113621435] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:39:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:39:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [790208] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:40:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:40:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [175277822] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:40:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [80] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:41:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1498042] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:41:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:48:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz [785849127] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:48:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [70] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:48:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1870634] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:48:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:48:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [59765930] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:48:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:48:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1058279] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:48:35 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:50:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz [207660687] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:50:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:50:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1180402] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:50:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:50:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz [58038828] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:50:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:50:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1035459] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:50:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:52:05 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz [202228594] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:52:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:52:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1115834] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:52:09 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:52:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz [58439864] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:52:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:52:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1033073] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:52:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:53:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz [207469504] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:53:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:54:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1169915] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:54:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:54:19 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [55091563] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:54:20 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:54:22 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1022214] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:54:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:55:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz [206335215] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:55:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:55:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1162437] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:55:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:55:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [61167754] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:55:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:56:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1062370] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-04 18:56:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-04 18:57:22 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz [216418425] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-04 18:57:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-04 18:57:25 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1206806] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-04 18:57:26 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-04 18:57:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [63953918] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-04 18:57:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/KK_HiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-04 18:57:51 U

So now the problem is this: [bwa_index] Update BWT... Killed

Apparently something in your system killed the BWA indexing process. Are you running on a system with restrictions on runtime or memory etc.? I recommend you run this script line-by-line manually to see what is going on.

OK. I'm working on a Macbook pro(Processor 2.3GHz Quad-Core Intel Core i7, Memory 32GB 3733MHz, Storage 1TB Flash Storage). This machine spec is not enough for calculation ??

2022年1月7日(金) 17:58 Niklas dAK @.***>:

So now the problem is this: [bwa_index] Update BWT... Killed

Apparently something in your system killed the BWA indexing process. Are you running on a system with restrictions on runtime or memory etc.? I recommend you run this script line-by-line manually to see what is going on.

— Reply to this email directly, view it on GitHub https://github.com/roland-rad-lab/MoCaSeq/issues/8#issuecomment-1007241474, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZ7I7YU7UJJT2FBCFSCGZDUU2TNDANCNFSM5KUX4ZPQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you authored the thread.Message ID: @.***>

32GB should be more than enough for BWA. But after managing the references, you should also change the default (32GB) of the MoCaSeq pipeline using -r 15 and probably also the number of threads with -t.

So again, I can not reproduce this error, so you will have to go into a script and execute line-by-line to find the exact error location (the FASTA should already be there and processed by the other script). The script you need to go through is: Preparation_GenerateBWAIndex.sh (check to repository folder in this repo)

You need the following variables:

VersionMouse=GRCm38.p6
config_file=/opt/MoCaSeq/config.sh
species=Mouse

Hi,

Maybe I could almost generate reference files using a higher spec machine. It seems there aren't apparent error from GetReferenceData.txt except one minor error (rm: cannot remove 'ref/GRCm38.p6/*.ebwt': No such file or) directory)

In Preparation_GetReferenceDataMouse,

rm "ref/"$VersionMouse"/.ebwt" should be rm "ref/"$VersionMouse"/"".ebwt"

Though, there are 2 files remaining in the temp folder("d501bb4941aa8736e3535d75aa4d5d4a" and "efb997c74eb841d4b0b7583791f2b721") after generating reference files, test run seems to be finished without error message.

However, when I tried S821-WES samples, I also had an error as belows. Files in results/bam folder were not created and the downstream analysis were not worked. In temp folder, 2 files and 2 folder remained (folder: sambamba-pid8303-markdup-ddcj, sambamba-pid8327-markdup-bajp file: S821-WES.Normal.cleaned.sorted.readgroups.bam, S821-WES.Tumor.cleaned.sorted.readgroups)

---- Matched BAM-files? ----

Fri Jan 14 18:54:03 UTC 2022 timestamp: 1642186443

+------------+

| FILE ERROR |

+------------+

Cannot access BAM file (/var/pipeline/S821-WES/results/bam/S821-WES.Tumor.bam).

It either does not exist or is not readable.

What is the problem ??

2022年1月10日(月) 18:10 Niklas dAK @.***>:

32GB should be more than enough for BWA. But after managing the references, you should also change the default (32GB) of the MoCaSeq pipeline using -r 15 and probably also the number of threads with -t.

So again, I can not reproduce this error, so you will have to go into a script and execute line-by-line to find the exact error location (the FASTA should already be there and processed by the other script). The script you need to go through is: Preparation_GenerateBWAIndex.sh (check to repository folder in this repo)

You need the following variables:

VersionMouse=GRCm38.p6 config_file=/opt/MoCaSeq/config.sh species=Mouse

— Reply to this email directly, view it on GitHub https://github.com/roland-rad-lab/MoCaSeq/issues/8#issuecomment-1008670169, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASZ7I75NY6LK7TQJQP6PK5LUVKO7JANCNFSM5KUX4ZPQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you authored the thread.Message ID: @.***>

---- Get reference data ---- ---- Generate reference data for Version GRCm38.p6 ---- Thu Jan 13 05:31:23 UTC 2022 ---- Copying over files from repository ---- Thu Jan 13 05:31:23 UTC 2022 ---- Downloading reference genome ---- Thu Jan 13 05:31:23 UTC 2022 2022-01-13 05:34:47 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz [860916719] -> "ref/GRCm38.p6/GCA_000001635.8_GRCm38.p6_genomic.fna.gz" [1] ---- Generate BWA Index ---- Thu Jan 13 05:35:12 UTC 2022 [bwa_index] Pack FASTA... 10.75 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=5451042740, availableWord=395555492 [BWTIncConstructFromPacked] 10 iterations done. 99999988 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999988 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999988 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999988 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999988 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999988 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999988 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999988 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999988 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999988 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999988 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999988 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999988 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999988 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999988 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999988 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999988 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999988 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999988 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999988 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099999988 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2199999988 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2299999988 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2399999988 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2499999988 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2599999988 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2699999988 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2799999988 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2899999988 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2999999988 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 3099999988 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 3199999988 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 3299999988 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 3399999988 characters processed. [BWTIncConstructFromPacked] 350 iterations done. 3499999988 characters processed. [BWTIncConstructFromPacked] 360 iterations done. 3599999988 characters processed. [BWTIncConstructFromPacked] 370 iterations done. 3699999988 characters processed. [BWTIncConstructFromPacked] 380 iterations done. 3799999988 characters processed. [BWTIncConstructFromPacked] 390 iterations done. 3899999988 characters processed. [BWTIncConstructFromPacked] 400 iterations done. 3999999988 characters processed. [BWTIncConstructFromPacked] 410 iterations done. 4099999988 characters processed. [BWTIncConstructFromPacked] 420 iterations done. 4199999988 characters processed. [BWTIncConstructFromPacked] 430 iterations done. 4299999988 characters processed. [BWTIncConstructFromPacked] 440 iterations done. 4399999988 characters processed. [BWTIncConstructFromPacked] 450 iterations done. 4499999988 characters processed. [BWTIncConstructFromPacked] 460 iterations done. 4599999988 characters processed. [BWTIncConstructFromPacked] 470 iterations done. 4699999988 characters processed. [BWTIncConstructFromPacked] 480 iterations done. 4799663908 characters processed. [BWTIncConstructFromPacked] 490 iterations done. 4891318228 characters processed. [BWTIncConstructFromPacked] 500 iterations done. 4972776836 characters processed. [BWTIncConstructFromPacked] 510 iterations done. 5045173444 characters processed. [BWTIncConstructFromPacked] 520 iterations done. 5109515732 characters processed. [BWTIncConstructFromPacked] 530 iterations done. 5166699284 characters processed. [BWTIncConstructFromPacked] 540 iterations done. 5217520164 characters processed. [BWTIncConstructFromPacked] 550 iterations done. 5262685908 characters processed. [BWTIncConstructFromPacked] 560 iterations done. 5302825316 characters processed. [BWTIncConstructFromPacked] 570 iterations done. 5338497268 characters processed. [BWTIncConstructFromPacked] 580 iterations done. 5370198564 characters processed. [BWTIncConstructFromPacked] 590 iterations done. 5398370724 characters processed. [BWTIncConstructFromPacked] 600 iterations done. 5423406180 characters processed. [BWTIncConstructFromPacked] 610 iterations done. 5445653684 characters processed. [bwt_gen] Finished constructing BWT in 613 iterations. [bwa_index] 1285.46 seconds elapse. [bwa_index] Update BWT... 6.60 sec [bwa_index] Pack forward-only FASTA... 7.60 sec [bwa_index] Construct SA from BWT and Occ... 640.34 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index -p ref/GRCm38.p6/primary_index/bwa_index -a bwtsw ref/GRCm38.p6/GRCm38.p6_primary.fna [main] Real time: 2014.985 sec; CPU: 1950.746 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 60 sequences (10059716 bp)... [M::process] read 30 sequences (10163001 bp)... [M::mem_process_seqs] Processed 60 reads in 94.750 CPU sec, 94.741 real sec [M::process] read 28 sequences (10373796 bp)... [M::mem_process_seqs] Processed 30 reads in 57.570 CPU sec, 57.554 real sec [M::process] read 28 sequences (10041032 bp)... [M::mem_process_seqs] Processed 28 reads in 81.409 CPU sec, 81.408 real sec [M::process] read 36 sequences (10701747 bp)... [M::mem_process_seqs] Processed 28 reads in 133.178 CPU sec, 133.161 real sec [M::process] read 10 sequences (10360147 bp)... [M::mem_process_seqs] Processed 36 reads in 168.193 CPU sec, 168.201 real sec [M::process] read 6 sequences (12242012 bp)... [M::mem_process_seqs] Processed 10 reads in 204.033 CPU sec, 204.210 real sec [M::process] read 4 sequences (12711166 bp)... [M::mem_process_seqs] Processed 6 reads in 266.320 CPU sec, 266.627 real sec [M::process] read 16 sequences (6800561 bp)... [M::mem_process_seqs] Processed 4 reads in 188.455 CPU sec, 188.615 real sec [M::mem_process_seqs] Processed 16 reads in 102.020 CPU sec, 102.166 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem ref/GRCm38.p6/primary_index/bwa_index ref/GRCm38.p6/haplotypes.fastq [main] Real time: 1309.058 sec; CPU: 1297.418 sec [bwa_index] Pack FASTA... 11.01 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=5637949096, availableWord=408706560 [BWTIncConstructFromPacked] 10 iterations done. 99999992 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999992 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999992 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999992 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999992 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999992 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999992 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999992 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999992 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999992 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999992 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999992 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999992 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999992 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999992 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999992 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999992 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999992 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999992 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999992 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099999992 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2199999992 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2299999992 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2399999992 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2499999992 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2599999992 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2699999992 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2799999992 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2899999992 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2999999992 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 3099999992 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 3199999992 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 3299999992 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 3399999992 characters processed. [BWTIncConstructFromPacked] 350 iterations done. 3499999992 characters processed. [BWTIncConstructFromPacked] 360 iterations done. 3599999992 characters processed. [BWTIncConstructFromPacked] 370 iterations done. 3699999992 characters processed. [BWTIncConstructFromPacked] 380 iterations done. 3799999992 characters processed. [BWTIncConstructFromPacked] 390 iterations done. 3899999992 characters processed. [BWTIncConstructFromPacked] 400 iterations done. 3999999992 characters processed. [BWTIncConstructFromPacked] 410 iterations done. 4099999992 characters processed. [BWTIncConstructFromPacked] 420 iterations done. 4199999992 characters processed. [BWTIncConstructFromPacked] 430 iterations done. 4299999992 characters processed. [BWTIncConstructFromPacked] 440 iterations done. 4399999992 characters processed. [BWTIncConstructFromPacked] 450 iterations done. 4499999992 characters processed. [BWTIncConstructFromPacked] 460 iterations done. 4599999992 characters processed. [BWTIncConstructFromPacked] 470 iterations done. 4699999992 characters processed. [BWTIncConstructFromPacked] 480 iterations done. 4799999992 characters processed. [BWTIncConstructFromPacked] 490 iterations done. 4899999992 characters processed. [BWTIncConstructFromPacked] 500 iterations done. 4999190584 characters processed. [BWTIncConstructFromPacked] 510 iterations done. 5089448040 characters processed. [BWTIncConstructFromPacked] 520 iterations done. 5169665112 characters processed. [BWTIncConstructFromPacked] 530 iterations done. 5240958232 characters processed. [BWTIncConstructFromPacked] 540 iterations done. 5304319720 characters processed. [BWTIncConstructFromPacked] 550 iterations done. 5360631560 characters processed. [BWTIncConstructFromPacked] 560 iterations done. 5410677672 characters processed. [BWTIncConstructFromPacked] 570 iterations done. 5455154744 characters processed. [BWTIncConstructFromPacked] 580 iterations done. 5494682040 characters processed. [BWTIncConstructFromPacked] 590 iterations done. 5529809992 characters processed. [BWTIncConstructFromPacked] 600 iterations done. 5561027784 characters processed. [BWTIncConstructFromPacked] 610 iterations done. 5588770200 characters processed. [BWTIncConstructFromPacked] 620 iterations done. 5613423720 characters processed. [BWTIncConstructFromPacked] 630 iterations done. 5635331768 characters processed. [bwt_gen] Finished constructing BWT in 632 iterations. [bwa_index] 1363.86 seconds elapse. [bwa_index] Update BWT... 6.80 sec [bwa_index] Pack forward-only FASTA... 8.06 sec [bwa_index] Construct SA from BWT and Occ... 643.17 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index -p ref/GRCm38.p6/bwa_index/GRCm38.p6 -a bwtsw ref/GRCm38.p6/GRCm38.p6.fna [main] Real time: 2098.691 sec; CPU: 2032.904 sec ---- Generate sequence dictionary ---- Thu Jan 13 07:49:08 UTC 2022 07:49:09.180 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jan 13 07:49:09 UTC 2022] CreateSequenceDictionary --OUTPUT ref/GRCm38.p6/GRCm38.p6.dict --REFERENCE ref/GRCm38.p6/GRCm38.p6.fna --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Jan 13 07:49:09 UTC 2022] Executing as @. on Linux 5.10.16.3-microsoft-standard-WSL2 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Thu Jan 13 07:49:24 UTC 2022] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.25 minutes. Runtime.totalMemory()=2884108288 ---- Generate exons covered by SureSelect ---- Thu Jan 13 07:49:24 UTC 2022 07:49:24.919 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jan 13 07:49:24 UTC 2022] BedToIntervalList --INPUT ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed --SEQUENCE_DICTIONARY ref/GRCm38.p6/GRCm38.p6.dict --OUTPUT ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --SORT true --UNIQUE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Jan 13 07:49:24 UTC 2022] Executing as @. on Linux 5.10.16.3-microsoft-standard-WSL2 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Thu Jan 13 07:49:26 UTC 2022] picard.util.BedToIntervalList done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=1617952768 ---- Downloading reference genome (for VEP) ---- Thu Jan 13 07:49:26 UTC 2022 2022-01-13 07:55:13 URL: ftp://ftp.ensembl.org/pub/release-96/variation/indexed_vep_cache/mus_musculus_vep_96_GRCm38.tar.gz [1463782096] -> "ref/GRCm38.p6/VEP/mus_musculus_vep_96_GRCm38.tar.gz" [1] ---- Generate customized Sanger DB ---- Thu Jan 13 07:55:43 UTC 2022 2022-01-13 07:55:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/ [29276] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/.listing" [1] 2022-01-13 07:56:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz [55622330] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 07:56:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 07:56:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [982936] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 07:56:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [88] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 07:56:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz [235966892] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 07:56:44 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 07:56:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1149443] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 07:56:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129P2_OlaHsd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 07:57:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [58575661] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 07:57:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 07:57:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1031914] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 07:57:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [87] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 07:57:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz [211532192] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 07:57:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 07:57:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1189688] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 07:57:53 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S1_SvImJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 07:58:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz [42189852] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 07:58:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 07:58:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [893761] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 07:58:05 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [88] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 07:58:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz [216725846] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 07:58:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 07:58:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1149402] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 07:58:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/129S5SvEvBrd.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 07:58:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [57351895] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 07:58:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 07:58:53 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1046489] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 07:58:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 07:59:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz [200078623] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 07:59:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [65] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 07:59:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1192350] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 07:59:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/A_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 07:59:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [57664949] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 07:59:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 07:59:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1047038] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 07:59:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:00:26 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz [203371139] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:00:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:00:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1208820] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:00:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/AKR_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:00:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [53342191] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:00:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:00:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1008737] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:01:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:01:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz [186363860] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:01:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:01:46 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1147448] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:01:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BALB_cJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:02:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [53890220] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:02:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [89] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:02:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1007726] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:02:07 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [93] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:02:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz [173804988] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:02:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:02:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1094144] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:02:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_TItpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BTBR_T__Itpr3tf_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:02:54 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [56916808] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:02:55 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:02:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1042711] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:02:58 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:03:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz [208769733] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:03:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:03:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1196235] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:03:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/BUB_BnJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:03:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz [46250554] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:03:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:03:46 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [994308] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:03:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:04:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz [175300582] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:04:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:04:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1123517] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:04:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeH.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:04:52 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [58710483] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:04:53 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [79] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:04:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1043079] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:04:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [83] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:05:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz [204244588] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:05:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [69] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:05:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1175979] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:05:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [73] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C3H_HeJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:05:46 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz [5929999] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:05:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:05:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [346568] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:05:51 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:05:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz [17321974] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:05:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:06:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [369781] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:06:01 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_10J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:06:03 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [1670145] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:06:04 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:06:06 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [243771] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:06:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:06:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz [7164392] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:06:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:06:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [491689] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:06:16 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:06:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [28977350] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:06:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:06:26 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [679229] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:06:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [85] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:06:44 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz [106537762] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:06:45 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:06:48 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [746658] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:06:49 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [75] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57BR_cdJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:06:56 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [28705588] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:06:57 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:06:59 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [690724] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:07:00 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:07:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz [105062300] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:07:25 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:07:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [743194] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:07:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C57L_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:07:37 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [33969296] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:07:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:07:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [763820] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:07:41 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:08:08 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz [113621435] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:08:09 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:08:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [790208] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:08:12 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/C58_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:08:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [175277822] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:08:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [80] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:08:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1498042] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:08:44 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [84] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:11:17 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz [785849127] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:11:18 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [70] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:11:21 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1870634] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:11:22 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [74] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:11:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz [59765930] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:11:33 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:11:35 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1058279] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:11:36 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [81] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:12:10 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz [207660687] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:12:11 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [67] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:12:14 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1180402] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:12:15 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [71] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/CBA_J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:12:27 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz [58038828] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:12:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:12:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1035459] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:12:32 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:13:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz [202228594] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:13:25 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:13:28 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1115834] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:13:29 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_1J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:13:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz [58439864] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:13:40 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:13:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1033073] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:13:44 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:14:19 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz [207469504] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:14:21 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:14:23 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1169915] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:14:24 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/DBA_2J.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:14:38 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [55091563] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:14:39 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [78] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:14:42 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1022214] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi" [1] 2022-01-13 08:14:43 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5 [82] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi.md5" [1] 2022-01-13 08:15:30 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz [206335215] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz" [1] 2022-01-13 08:15:31 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5 [68] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.md5" [1] 2022-01-13 08:15:34 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi [1162437] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi" [1] 2022-01-13 08:15:35 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5 [72] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/FVB_NJ.mgp.v5.snps.dbSNP142.vcf.gz.tbi.md5" [1] 2022-01-13 08:15:46 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz [61167754] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz" [1] 2022-01-13 08:15:47 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5 [77] -> "/var/pipeline/temp/ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.md5" [1] 2022-01-13 08:15:50 URL: ftp://ftp-mouse.sanger.ac.uk//REL-1505-SNPs_Indels/strain_specific_vcfs/I_LnJ.mgp.v5.indels.dbSNP142.normed.vcf.gz.tbi [1062370] -> "/var/pipeline/temp/ftp-mo

Could you please provide me the entire S821-WES/QC/S821-WES.report.txt file? Please attach it as a file, do not copy the raw text in here.

Hi,

Actually, I tried again and this time "Cannot access BAM file (/var/pipeline/S821-WES/results/bam/S821-WES.Tumor.bam)." error was not occured but other error seems to be happen (I've ovrewritten the first run of S821-WES.report.txt....).

Also, I thought "--test run" worked without problem but several error seems to be happen.

I attach "MoCaSeq_Test.report.txt" and 2nd time run of "S821-WES.report.txt"

Thaks in advance MoCaSeq_Test.report.txt S821-WES.report.txt .

roland-rad-lab / MoCaSeq

Cannot access BAM file #8