Open GATKSupportTeam opened 4 years ago
Hi @lbergelson as discussed during the office hrs, I created this issue ticket to brainstorm ideas around how to check for either "@"/"#" identifiers in the interval list file.
I think that this is a GATK (not picard) problem.
It's a barclay problem. We patched barclay to add a warning in the case of an incorrectly labelled interval.list file which should mitigate it. Waiting on a barclay release though.
Huh, a mysterious stranger with insight into the problem. Lets all forget about whoever that person may be. I'm pretty sure they're correct in their assessment though..
lol
On Sun, Mar 15, 2020 at 8:03 PM Louis Bergelson notifications@github.com wrote:
Huh, a mysterious stranger with insight into the problem. Lets all forget about whoever that person may be. I'm pretty sure they're correct in their assessment though..
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Error due to
interval.list
instead ofinterval_list
suffixLink: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056676692-HS-PENALTY-20X-is-1-on-one-version-of-GATK-crashes-on-newest-version-
--
When running GATK 4.0.0.0 this works fine but I get a HS_PENALTY_20X of -1
It errors out on GATK v4.1.4.1
I assume a -1 for HS_PENALTY_20X is incorrect?
# CONFIRMING FILES EXIST
=================================
3.8G /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3f_MARK_DUPLICATES_FALSE/19065WBC_fixmate_novosort_dupsrmFalse.bam
54M /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.bait.interval.list
45M /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.target.interval.list
# GATK VERSION
=================================
The Genome Analysis Toolkit (GATK) v4.1.4.1
HTSJDK Version: 2.21.0
Picard Version: 2.21.2
Using GATK jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk-newest/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk-newest/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar --version
# GATK COMMAND
gatk CollectHsMetrics --INPUT /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3f_MARK_DUPLICATES_FALSE/19065WBC_fixmate_novosort_dupsrmFalse.bam --OUTPUT TEMP_NEW/19065WBC_fixmate_novosort_dupsrm.bam_hs_metrics.txt --BAIT_INTERVALS /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.bait.interval.list --TARGET_INTERVALS /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.target.interval.list
=================================
22:29:20.348 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk-newest/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Feb 03 22:29:20 EST 2020] CollectHsMetrics --BAIT_INTERVALS /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.bait.interval.list --TARGET_INTERVALS /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.target.interval.list --INPUT /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3f_MARK_DUPLICATES_FALSE/19065WBC_fixmate_novosort_dupsrmFalse.bam --OUTPUT TEMP_NEW/19065WBC_fixmate_novosort_dupsrm.bam_hs_metrics.txt --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --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
Feb 03, 2020 10:29:20 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Mon Feb 03 22:29:20 EST 2020] Executing as nowackj1@ridus004.ind.roche.com on Linux 3.10.0-1062.1.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.4.1
[Mon Feb 03 22:29:20 EST 2020] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2972712960
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMException: Cannot read non-existent file: file:///data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/@HD%09VN:1.4%09SO:unsorted
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:498)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:485)
at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:115)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Using GATK jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk-newest/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk-newest/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar CollectHsMetrics --INPUT /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3f_MARK_DUPLICATES_FALSE/19065WBC_fixmate_novosort_dupsrmFalse.bam --OUTPUT TEMP_NEW/19065WBC_fixmate_novosort_dupsrm.bam_hs_metrics.txt --BAIT_INTERVALS /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.bait.interval.list --TARGET_INTERVALS /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3d_INTERVALS/19065WBC_R1.target.interval.list
(created from Zendesk ticket #4552)
gz#4552