sarek in slurm : issue - Githubissues

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

MIT License

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SBATCH --error=/TEST/sarek300%j.err

nextflow run /TEST/sarek/main.nf -profile docker --input /TEST/samplesheet.csv --genome GATK.GRCh38 --outdir /TEST/results/ ########## The error I am getting is , cat sarek_1.err tput: terminal attributes: No such device or address tput: terminal attributes: No such device or address tput: terminal attributes: No such device or address tput: terminal attributes: No such device or address tput: terminal attributes: No such device or address

cat sarek_1.out WARN: There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAR EK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS? ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)'

the sample sheet , patient,sample,lane,fastq_1,fastq_2 I1,test_sample,lane_1,test_sample_R1_xxx.fastq.gz,test_sample_R2_xxx.fastq.gz

Can anyone give a solution to this.

Jul-27 13:49:35.585 [main] DEBUG nextflow.cli.Launcher - $> nextflow run/TEST/sarek/main.nf -profile docker --input/TEST/samplesheet.csv --genome GATK.GRCh38 --outdir/TEST/results/ Jul-27 13:49:35.764 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2 Jul-27 13:49:35.782 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3 Jul-27 13:49:35.801 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jul-27 13:49:35.802 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jul-27 13:49:35.805 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Jul-27 13:49:35.815 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jul-27 13:49:35.834 [main] DEBUG nextflow.config.ConfigBuilder - Found config base:/TEST/sarek/nextflow.config Jul-27 13:49:35.836 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file:/TEST/sarek/nextflow.config Jul-27 13:49:35.859 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker` Jul-27 13:49:38.951 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, uge, rosalind_uge, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, use_gatk_spark, eddie, medair, alignment_to_fastq, biowulf, apptainer, bi, bigpurple, sbc_sharc, adcra, cedars, tools, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, targeted, icr_davros, ceres, save_bam_mapped, munin, arm, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, wustl_htcf, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, ebi_codon, cheaha, xanadu, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, dkfz, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, hypatia, psmn, umi, eva, markduplicates_bam, fgcz, conda, crg, singularity, uw_hyak_pedslabs, prince, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, test_cache, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, seawulf, fub_curta, uct_hpc, aws_tower, binac] Jul-27 13:49:39.017 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Jul-27 13:49:39.042 [main] INFO nextflow.cli.CmdRun - Launching `/TEST/sarek/main.nf` [infallible_rutherford] DSL2 - revision: c2275107d1 Jul-27 13:49:39.043 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jul-27 13:49:39.043 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Jul-27 13:49:39.049 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store:/.nextflow/secrets/store.json Jul-27 13:49:39.053 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@990b86b] - activable => nextflow.secret.LocalSecretsProvider@990b86b Jul-27 13:49:39.122 [main] DEBUG nextflow.Session - Session UUID: e9022e61-1a32-4641-af9c-0644792f3f3f Jul-27 13:49:39.122 [main] DEBUG nextflow.Session - Run name: infallible_rutherford Jul-27 13:49:39.123 [main] DEBUG nextflow.Session - Executor pool size: 8 Jul-27 13:49:39.133 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jul-27 13:49:39.154 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.2 build 5870 Created: 08-06-2023 08:29 UTC System: Linux 5.10.144-127.601.amzn2.x86_64 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.7+7-LTS Encoding: UTF-8 (UTF-8) Process: 20824@queue1-st-r54xlarge-1 [10.70.135.98] CPUs: 8 - Mem: 124.4 GB (27.2 GB) - Swap: 24 GB (18.5 GB) Jul-27 13:49:39.218 [main] DEBUG nextflow.Session - Work-dir:/TEST/work [nfs] Jul-27 13:49:39.218 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory:/TEST/sarek/bin Jul-27 13:49:39.232 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jul-27 13:49:39.244 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jul-27 13:49:39.358 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jul-27 13:49:39.367 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Jul-27 13:49:39.607 [main] DEBUG nextflow.Session - Session start Jul-27 13:49:39.611 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file:/TEST/results/pipeline_info/execution_trace_2023-07-27_13-49-37.txt Jul-27 13:49:39.627 [main] DEBUG nextflow.Session - Using default localLib path:/TEST/sarek/lib Jul-27 13:49:39.639 [main] DEBUG nextflow.Session - Adding to the classpath library:/TEST/sarek/lib Jul-27 13:49:39.640 [main] DEBUG nextflow.Session - Adding to the classpath library:/TEST/sarek/lib/nfcore_external_java_deps.jar Jul-27 13:49:40.568 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jul-27 13:49:40.639 [main] INFO nextflow.Nextflow - -[2m----------------------------------------------------[0m- [0;32m,--.[0;30m/[0;32m,-.[0m [0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m [0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m [0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m [0;32m`._,._,'[0m [0;37m ____[0m [0;37m .´ _ `.[0m [0;37m / [0;32m|\[0m`-_ \[0m [0;34m __ __ ___ [0m [0;37m | [0;32m| \[0m `-|[0m [0;34m|__` /\ |__) |__ |__/[0m [0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m [0;37m `[0;32m|[0m____[0;32m\[0m´[0m [0;35m nf-core/sarek v3.2.3[0m -[2m----------------------------------------------------[0m- [1mCore Nextflow options[0m [0;34mrunName : [0;32minfallible_rutherford[0m [0;34mcontainerEngine : [0;32mdocker[0m [0;34mlaunchDir : [0;32m/TEST[0m [0;34mworkDir : [0;32m/TEST/work[0m [0;34mprojectDir : [0;32m/TEST/sarek[0m [0;34muserName : [0;32mjgs8049[0m [0;34mprofile : [0;32mdocker[0m [0;34mconfigFiles : [0;32m/TEST/sarek/nextflow.config[0m [1mInput/output options[0m [0;34minput : [0;32m/TEST/samplesheet.csv[0m [0;34moutdir : [0;32m/TEST/results/[0m [1mMain options[0m [0;34mintervals : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed[0m [1mVariant Calling[0m [0;34mcf_chrom_len : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len[0m [0;34mpon : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz[0m [0;34mpon_tbi : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi[0m [1mReference genome options[0m [0;34mascat_genome : [0;32mhg38[0m [0;34mascat_alleles : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip[0m [0;34mascat_loci : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip[0m [0;34mascat_loci_gc : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip[0m [0;34mascat_loci_rt : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip[0m [0;34mbwa : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/[0m [0;34mbwamem2 : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/[0m [0;34mchr_dir : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes[0m [0;34mdbsnp : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz[0m [0;34mdbsnp_tbi : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi[0m [0;34mdbsnp_vqsr : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m [0;34mdict : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict[0m [0;34mdragmap : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/[0m [0;34mfasta : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta[0m [0;34mfasta_fai : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai[0m [0;34mgermline_resource : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz[0m [0;34mgermline_resource_tbi: [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi[0m [0;34mknown_indels : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz[0m [0;34mknown_indels_tbi : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi[0m [0;34mknown_indels_vqsr : [0;32m--resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz[0m [0;34mknown_snps : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz[0m [0;34mknown_snps_tbi : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi[0m [0;34mknown_snps_vqsr : [0;32m--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz[0m [0;34mmappability : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem[0m [0;34msnpeff_db : [0;32m105[0m [0;34msnpeff_genome : [0;32mGRCh38[0m [0;34msnpeff_version : [0;32m5.1[0m [0;34mvep_genome : [0;32mGRCh38[0m [0;34mvep_species : [0;32mhomo_sapiens[0m [0;34mvep_cache_version : [0;32m108[0m [0;34mvep_version : [0;32m108.2[0m [0;34migenomes_base : [0;32ms3://ngi-igenomes/igenomes[0m !! Only displaying parameters that differ from the pipeline defaults !! Displaying all reference genome parameters -[2m----------------------------------------------------[0m- If you use nf-core/sarek for your analysis please cite: * The pipeline https://doi.org/10.12688/f1000research.16665.2 https://doi.org/10.5281/zenodo.4468605 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/sarek/blob/master/CITATIONS.md -[2m----------------------------------------------------[0m- Jul-27 13:49:44.069 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 1.16.2 Jul-27 13:49:44.107 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@1.16.2' resolved Jul-27 13:49:44.107 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@1.16.2' Jul-27 13:49:44.145 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@1.16.2 Jul-27 13:49:44.169 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3] Jul-27 13:49:44.169 [main] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip Jul-27 13:49:44.187 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider Jul-27 13:49:44.199 [main] DEBUG nextflow.Global - Using AWS credential defined in `default` section in file:/.aws/credentials Jul-27 13:49:44.202 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {secret_key=JYDgz1.., region=us-east-1, max_error_retry=5, access_key=AKIAVI..} Jul-27 13:49:44.517 [main] DEBUG com.upplication.s3fs.AmazonS3Client - Setting S3 glacierRetrievalTier=null Jul-27 13:50:05.291 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Jul-27 13:50:05.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Jul-27 13:50:05.302 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.302 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.306 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Jul-27 13:50:05.310 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=124.4 GB; capacity=8; pollInterval=100ms; dumpInterval=5m Jul-27 13:50:05.365 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Jul-27 13:50:05.366 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Jul-27 13:50:05.370 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.370 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.376 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Jul-27 13:50:05.376 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Jul-27 13:50:05.380 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.380 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.383 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Jul-27 13:50:05.383 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Jul-27 13:50:05.385 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.385 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.389 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Jul-27 13:50:05.389 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Jul-27 13:50:05.391 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.391 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.395 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Jul-27 13:50:05.396 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Jul-27 13:50:05.398 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.398 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jul-27 13:50:05.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jul-27 13:50:05.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jul-27 13:50:05.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jul-27 13:50:05.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jul-27 13:50:05.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jul-27 13:50:05.415 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jul-27 13:50:05.415 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jul-27 13:50:05.417 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.417 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.422 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jul-27 13:50:05.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jul-27 13:50:05.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jul-27 13:50:05.424 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jul-27 13:50:05.426 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.426 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jul-27 13:50:05.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jul-27 13:50:05.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jul-27 13:50:05.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jul-27 13:50:05.433 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.433 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.436 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jul-27 13:50:05.436 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jul-27 13:50:05.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jul-27 13:50:05.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jul-27 13:50:05.439 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.439 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Jul-27 13:50:05.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Jul-27 13:50:05.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Jul-27 13:50:05.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Jul-27 13:50:05.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.491 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Jul-27 13:50:05.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Jul-27 13:50:05.494 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Jul-27 13:50:05.494 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Jul-27 13:50:05.496 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.496 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Jul-27 13:50:05.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Jul-27 13:50:05.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Jul-27 13:50:05.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Jul-27 13:50:05.503 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.503 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.508 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Jul-27 13:50:05.509 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Jul-27 13:50:05.510 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Jul-27 13:50:05.510 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Jul-27 13:50:05.512 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.512 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.559 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Jul-27 13:50:05.560 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Jul-27 13:50:05.562 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.562 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.591 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jul-27 13:50:05.592 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jul-27 13:50:05.593 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jul-27 13:50:05.593 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jul-27 13:50:05.596 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.596 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.604 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Jul-27 13:50:05.604 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Jul-27 13:50:05.605 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Jul-27 13:50:05.607 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.607 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.626 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Jul-27 13:50:05.627 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Jul-27 13:50:05.630 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.630 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Jul-27 13:50:05.642 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Jul-27 13:50:05.646 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.646 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.651 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Jul-27 13:50:05.653 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Jul-27 13:50:05.657 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.657 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.662 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Jul-27 13:50:05.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Jul-27 13:50:05.668 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.668 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.685 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Jul-27 13:50:05.687 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Jul-27 13:50:05.690 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.691 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.697 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Jul-27 13:50:05.699 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Jul-27 13:50:05.702 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.702 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.707 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Jul-27 13:50:05.709 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Jul-27 13:50:05.712 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.713 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.720 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Jul-27 13:50:05.720 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Jul-27 13:50:05.721 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.721 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC Jul-27 13:50:05.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC Jul-27 13:50:05.733 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.733 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.750 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP Jul-27 13:50:05.751 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP Jul-27 13:50:05.752 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.752 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.773 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jul-27 13:50:05.773 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jul-27 13:50:05.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jul-27 13:50:05.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jul-27 13:50:05.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jul-27 13:50:05.775 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.775 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jul-27 13:50:05.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jul-27 13:50:05.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jul-27 13:50:05.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jul-27 13:50:05.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jul-27 13:50:05.780 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.780 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.793 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jul-27 13:50:05.793 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jul-27 13:50:05.794 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jul-27 13:50:05.794 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.795 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.819 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Jul-27 13:50:05.819 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Jul-27 13:50:05.819 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Jul-27 13:50:05.820 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.820 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.834 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Jul-27 13:50:05.835 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Jul-27 13:50:05.835 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.835 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.856 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH Jul-27 13:50:05.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH Jul-27 13:50:05.858 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.858 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.875 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM Jul-27 13:50:05.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Jul-27 13:50:05.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Jul-27 13:50:05.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Jul-27 13:50:05.877 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.877 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Jul-27 13:50:05.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Jul-27 13:50:05.904 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Jul-27 13:50:05.905 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.905 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.911 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Jul-27 13:50:05.911 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Jul-27 13:50:05.911 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Jul-27 13:50:05.912 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.912 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.930 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Jul-27 13:50:05.931 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Jul-27 13:50:05.931 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Jul-27 13:50:05.932 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.932 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.941 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM Jul-27 13:50:05.942 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM Jul-27 13:50:05.943 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.943 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Jul-27 13:50:05.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Jul-27 13:50:05.949 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Jul-27 13:50:05.950 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.950 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.964 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS Jul-27 13:50:05.965 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS Jul-27 13:50:05.965 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.965 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.973 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Jul-27 13:50:05.973 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Jul-27 13:50:05.973 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Jul-27 13:50:05.974 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.974 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:05.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Jul-27 13:50:05.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Jul-27 13:50:05.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM_RECAL` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Jul-27 13:50:05.989 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:05.989 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:06.012 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jul-27 13:50:06.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jul-27 13:50:06.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jul-27 13:50:06.014 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:06.014 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:06.074 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC Jul-27 13:50:06.074 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC Jul-27 13:50:06.075 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-27 13:50:06.075 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-27 13:50:06.082 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKEGRAPH, CONTROLFREEC_MAKEGRAPH, SAMTOOLS_VIEW_MAP_MAP, SVDB_MERGE, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS, MERGE_GENOTYPEGVCFS, SAMTOOLS_MERGE, BWA_MEM, GATK4_APPLYBQSR_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE, ADD_INFO_TO_VCF, BUILD_INTERVALS, SAMTOOLS_VIEW_UNMAP_UNMAP, FILTERVARIANTTRANCHES, CAT_FASTQ, CONTROLFREEC_FREEC2CIRCOS, SAMTOOLS_STATS, INDEX_MERGE_BAM, MUTECT2, GATK4_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR, TABIX_EXT_VCF, VCFTOOLS, NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX, TABIX_TABIX, FASTQC, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM, MULTIQC, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY, TABIX_GERMLINE_RESOURCE, ASSESS_SIGNIFICANCE, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT, CALLUMICONSENSUS, TABIX_KNOWN_SNPS, CAT_CAT, NFCORE_SAREK:SAREK:FASTQC, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON, GATHERPILEUPSUMMARIES_NORMAL, SAMTOOLS_FAIDX, MERGE_BAM, STRELKA_GERMLINE, TIDDIT_SV, GETPILEUPSUMMARIES_TUMOR, STRELKA_SINGLE, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES, SAMTOOLS_BAM2FQ, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP, BWAMEM2_MEM, VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE, UNZIP_ALLELES, BCFTOOLS_STATS, GATK4_GETPILEUPSUMMARIES, LEARNREADORIENTATIONMODEL, GATK4_VARIANTRECALIBRATOR, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS, FASTP, NFCORE_SAREK:SAREK:CRAM_TO_BAM, MERGE_FREEBAYES, MSISENSORPRO_SCAN, GATK4_MERGEVCFS, GATHERPILEUPSUMMARIES_TUMOR, UNTAR, TABIX_BGZIPTABIX_INTERVAL_SPLIT, MERGE_DEEPVARIANT_VCF, CNVKIT_REFERENCE, ENSEMBLVEP_VEP, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC, FREEC2BED, UNZIP_LOCI, GATK4_FILTERVARIANTTRANCHES, TABIX_KNOWN_INDELS, SNPEFF_SNPEFF, CREATE_INTERVALS_BED, BAM_TO_CRAM, GROUPREADSBYUMI, NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN, BAM_TO_CRAM_MAPPING, FASTQTOBAM, CONTROLFREEC_FREEC, NFCORE_SAREK:SAREK:MULTIQC, GATK4_ESTIMATELIBRARYCOMPLEXITY, CRAM_TO_BAM, BWAMEM1_MEM, GATK4_APPLYVQSR_SNP, VCFTOOLS_TSTV_QUAL, GATK4_APPLYBQSR, GATK4_BASERECALIBRATOR, GERMLINE_VCFS_CONCAT, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM, NFCORE_SAREK:SAREK:FASTP, TABIX_DBSNP, FILTERMUTECTCALLS, CNNSCOREVARIANTS, SNPEFF_DOWNLOAD, GATK4_LEARNREADORIENTATIONMODEL, MANTA_GERMLINE, BWA_INDEX, INDEX_MARKDUPLICATES, GERMLINE_VCFS_CONCAT_SORT, MERGE_HAPLOTYPECALLER, STRELKA_SOMATIC, FREEC_SOMATIC, GATK4_MUTECT2, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR, VARIANTRECALIBRATOR_INDEL, MERGE_BCFTOOLS_MPILEUP, CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM, FGBIO_FASTQTOBAM, ENSEMBLVEP_DOWNLOAD, CRAM_TO_BAM_RECAL, GATK4_GATHERBQSRREPORTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT, TABIX_BGZIPTABIX, GATK4_MARKDUPLICATES_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES, GATK4_CREATESEQUENCEDICTIONARY, MERGE_DEEPVARIANT_GVCF, CALCULATECONTAMINATION, COLLATE_FASTQ_MAP, TABIX_VC_FREEBAYES, MOSDEPTH, MERGE_STRELKA_INDELS, COLLATE_FASTQ_UNMAP, UNZIP, UNZIP_GC, VCFTOOLS_TSTV_COUNT, GATK4_MERGEMUTECTSTATS, CAT_MPILEUP, CONTROLFREEC_ASSESSSIGNIFICANCE, MANTA_TUMORONLY, BWAMEM2_INDEX, MERGE_STRELKA_SNVS, SAMTOOLS_VIEW_MAP_UNMAP, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI, MERGE_STRELKA, BCFTOOLS_CONCAT, SAMTOOLS_INDEX, MERGE_CRAM, GATK4_CNNSCOREVARIANTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP, TABIX_BGZIP_TIDDIT_SV, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED, TABIX_PON, VARIANTRECALIBRATOR_SNP, TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS, UNTAR_CHR_DIR, FREEC_TUMORONLY, SAMBLASTER, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH, FREEBAYES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP, GATHERPILEUPSUMMARIES, NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL, INDEX_CRAM, SAMTOOLS_MPILEUP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ, BCFTOOLS_SORT, MANTA_SOMATIC, NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS, GATK4_FILTERMUTECTCALLS, MERGE_VQSR, MUTECT2_PAIRED, BWAMEM1_INDEX, GATK4_GATHERPILEUPSUMMARIES, DRAGMAP_HASHTABLE, CNVKIT_ANTITARGET, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN, GATK4_MARKDUPLICATES, SAMTOOLS_VIEW_UNMAP_MAP, SAMTOOLS_CONVERT, TABIX_GERMLINE_VCFS_CONCAT_SORT, CONTROLFREEC_FREEC2BED, MERGE_STRELKA_GENOME, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP, BAM2FASTQ, UNZIP_RT, MERGEMUTECTSTATS, SAMTOOLS_COLLATEFASTQ, GATK4_APPLYVQSR, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM, GATK4_CALCULATECONTAMINATION, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS, DEEPVARIANT, GATK4_GENOTYPEGVCFS, MSISENSORPRO_MSI_SOMATIC, FREEC2CIRCOS, DRAGMAP_ALIGN, GATK4_INTERVALLISTTOBED, GATK4_APPLYVQSR_INDEL, FGBIO_GROUPREADSBYUMI, BCFTOOLS_MPILEUP, SAMTOOLS_VIEW, CNVKIT_BATCH, FGBIO_CALLMOLECULARCONSENSUSREADS, GETPILEUPSUMMARIES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP, GETPILEUPSUMMARIES_NORMAL, GATK4_GENOMICSDBIMPORT, MERGE_MUTECT2, GATK4_BASERECALIBRATOR_SPARK, ASCAT Jul-27 13:50:06.117 [main] WARN nextflow.Session - There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS? Jul-27 13:50:06.120 [main] DEBUG nextflow.Session - Igniting dataflow network (118) Jul-27 13:50:06.131 [PathVisitor-5] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz; options: [:] Jul-27 13:50:06.137 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Jul-27 13:50:06.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Jul-27 13:50:06.139 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Jul-27 13:50:06.141 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Jul-27 13:50:06.142 [PathVisitor-8] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi; options: [:] Jul-27 13:50:06.144 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jul-27 13:50:06.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jul-27 13:50:06.146 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Jul-27 13:50:06.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jul-27 13:50:06.148 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC Jul-27 13:50:06.148 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Jul-27 13:50:06.148 [main] DEBUG nextflow.Session - Session await Jul-27 13:50:06.278 [Actor Thread 35] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.015 s; total time: 0.016 s Jul-27 13:50:06.278 [Actor Thread 32] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.015 s; total time: 0.016 s Jul-27 13:50:06.306 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Saved collect-files list to:/TEST/work/collect-file/85dfae1cdf7579c5dea01ebc5c3c19e7 Jul-27 13:50:06.309 [Actor Thread 35] DEBUG nextflow.file.FileCollector - Saved collect-files list to:/TEST/work/collect-file/e34a121d36855bb8f9b64ea112f1b5f2 Jul-27 13:50:06.313 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6784443329940595637 Jul-27 13:50:06.313 [Actor Thread 35] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-12903132534304596716 Jul-27 13:50:06.320 [Task submitter] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1); work-dir=/TEST/work/4e/6a7d3647747c9a7ce20df8c8197609 error [nextflow.exception.ProcessUnrecoverableException]: Process requirement exceeds available CPUs -- req: 12; avail: 8 Jul-27 13:50:06.334 [Task submitter] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)' -- Cause: java.nio.file.NoSuchFileException:/TEST/work/4e/6a7d3647747c9a7ce20df8c8197609/.command.log Jul-27 13:50:06.335 [Task submitter] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)' Caused by: Process requirement exceeds available CPUs -- req: 12; avail: 8 Command executed: [ ! -f test_sample-lane_1_1.fastq.gz ] && ln -sf dummy_n_R1_xxx.fastq.gz test_sample-lane_1_1.fastq.gz [ ! -f test_sample-lane_1_2.fastq.gz ] && ln -sf dummy_n_R2_xxx.fastq.gz test_sample-lane_1_2.fastq.gz fastp \ --in1 test_sample-lane_1_1.fastq.gz \ --in2 test_sample-lane_1_2.fastq.gz \ --out1 test_sample-lane_1_1.fastp.fastq.gz \ --out2 test_sample-lane_1_2.fastp.fastq.gz \ --json test_sample-lane_1.fastp.json \ --html test_sample-lane_1.fastp.html \ \ \ \ --thread 12 \ --detect_adapter_for_pe \ --disable_adapter_trimming --split_by_lines 200000000 \ 2> test_sample-lane_1.fastp.log cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:FASTP": fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g") END_VERSIONS Command exit status: - Command output: (empty) Work dir: /TEST/work/4e/6a7d3647747c9a7ce20df8c8197609 Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line Jul-27 13:50:06.337 [Task submitter] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Jul-27 13:50:06.341 [main] DEBUG nextflow.Session - Session await > all processes finished Jul-27 13:50:06.341 [main] DEBUG nextflow.Session - Session await > all barriers passed Jul-27 13:50:06.343 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.343 [Actor Thread 30] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.343 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.343 [Actor Thread 11] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.343 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.343 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.343 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 22] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.344 [Actor Thread 21] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.345 [Actor Thread 20] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.345 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.346 [Actor Thread 21] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Jul-27 13:50:06.346 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.347 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.347 [Actor Thread 21] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Jul-27 13:50:06.347 [Actor Thread 32] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Jul-27 13:50:06.348 [Actor Thread 6] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Jul-27 13:50:06.348 [Actor Thread 13] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Jul-27 13:50:06.350 [Actor Thread 43] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:MULTIQC; work-dir=null error [java.lang.IllegalStateException]: Cannot obtain the semaphore to fork operator's body. Jul-27 13:50:06.351 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m- Jul-27 13:50:06.355 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=2; submittedCount=0; runningCount=-1; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=-12; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] Jul-27 13:50:06.355 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jul-27 13:50:06.363 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jul-27 13:50:06.381 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":null,"process":"FASTP","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}] Jul-27 13:50:06.990 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Jul-27 13:50:07.394 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jul-27 13:50:07.394 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@1.16.2' Jul-27 13:50:07.394 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon Jul-27 13:50:07.468 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Jul-27 13:50:07.470 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Hi , after adding the custom config ,

process {
  executor = 'slurm'
}

params {
  max_memory = 120.GB
  max_cpus = 8
  max_time = '72.h'

}

and updating bash,

#!/bin/bash
#SBATCH --qos=standard
#SBATCH --job-name=cd_301
#SBATCH --nodes=1
#SBATCH --tasks=2
#SBATCH --cpus-per-task=8
#SBATCH --tasks-per-node=1
#SBATCH --output=/mnt/efs/home/jgs8049/TEST/sarek_301_%j.out
#SBATCH --chdir=/mnt/efs/home/jgs8049/TEST/
#SBATCH --error=/mnt/efs/home/jgs8049/TEST/sarek_300_%j.err

nextflow run /mnt/efs/home/jgs8049/TEST/sarek/main.nf  -c my_config.config -profile docker --input /mnt/efs/home/jgs8049/TEST/samplesheet.csv --genome GATK.GRCh38 --outdir /mnt/efs/home/jgs8049/TEST/results/ --max_cpus 8

########
I am getting the error 

.nextflow .log
##########
Jul-28 07:32:53.553 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /TEST/sarek/main.nf -c my_config.config -profile docker --input /TEST/samplesheet.csv --genome GATK.GRCh38 --outdir /TEST/results/ --max_cpus 8
Jul-28 07:32:53.723 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.2
Jul-28 07:32:53.741 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3
Jul-28 07:32:53.757 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-28 07:32:53.758 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-28 07:32:53.761 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jul-28 07:32:53.772 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jul-28 07:32:53.786 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /TEST/sarek/nextflow.config
Jul-28 07:32:53.792 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /TEST/my_config.config
Jul-28 07:32:53.792 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /TEST/sarek/nextflow.config
Jul-28 07:32:53.792 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /TEST/my_config.config
Jul-28 07:32:53.813 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-28 07:32:57.083 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-28 07:32:57.104 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, uge, rosalind_uge, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, use_gatk_spark, eddie, medair, alignment_to_fastq, biowulf, apptainer, bi, bigpurple, sbc_sharc, adcra, cedars, tools, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, targeted, icr_davros, ceres, save_bam_mapped, munin, arm, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, wustl_htcf, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, ebi_codon, cheaha, xanadu, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, dkfz, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, hypatia, psmn, umi, eva, markduplicates_bam, fgcz, conda, crg, singularity, uw_hyak_pedslabs, prince, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, test_cache, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, seawulf, fub_curta, uct_hpc, aws_tower, binac]
Jul-28 07:32:57.147 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jul-28 07:32:57.166 [main] INFO  nextflow.cli.CmdRun - Launching `/TEST/sarek/main.nf` [berserk_yonath] DSL2 - revision: c2275107d1
Jul-28 07:32:57.167 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-28 07:32:57.168 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-28 07:32:57.172 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /.nextflow/secrets/store.json
Jul-28 07:32:57.174 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7109b603] - activable => nextflow.secret.LocalSecretsProvider@7109b603
Jul-28 07:32:57.247 [main] DEBUG nextflow.Session - Session UUID: 43d5f3c7-a484-4b55-94a9-cb55beaee6d6
Jul-28 07:32:57.247 [main] DEBUG nextflow.Session - Run name: berserk_yonath
Jul-28 07:32:57.248 [main] DEBUG nextflow.Session - Executor pool size: 8
Jul-28 07:32:57.257 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-28 07:32:57.275 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.2 build 5870
  Created: 08-06-2023 08:29 UTC 
  System: Linux 5.10.144-127.601.amzn2.x86_64
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.7+7-LTS
  Encoding: UTF-8 (UTF-8)
  Process: 30396@queue1-st-r54xlarge-1 [10.70.135.98]
  CPUs: 8 - Mem: 124.4 GB (27.2 GB) - Swap: 24 GB (18.5 GB)
Jul-28 07:32:57.326 [main] DEBUG nextflow.Session - Work-dir: /TEST/work [nfs]
Jul-28 07:32:57.326 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /TEST/sarek/bin
Jul-28 07:32:57.336 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-28 07:32:57.366 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-28 07:32:57.459 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-28 07:32:57.468 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Jul-28 07:32:57.653 [main] DEBUG nextflow.Session - Session start
Jul-28 07:32:57.657 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /TEST/results/pipeline_info/execution_trace_2023-07-28_07-32-55.txt
Jul-28 07:32:57.672 [main] DEBUG nextflow.Session - Using default localLib path: /TEST/sarek/lib
Jul-28 07:32:57.678 [main] DEBUG nextflow.Session - Adding to the classpath library: /TEST/sarek/lib
Jul-28 07:32:57.679 [main] DEBUG nextflow.Session - Adding to the classpath library: /TEST/sarek/lib/nfcore_external_java_deps.jar
Jul-28 07:32:58.574 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-28 07:32:58.632 [main] INFO  nextflow.Nextflow - 

-[2m----------------------------------------------------[0m-
                                        [0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m        ___     __   __   __   ___     [0;32m/,-._.--~'[0m
[0;34m  |\ | |__  __ /  ` /  \ |__) |__         [0;33m}  {[0m
[0;34m  | \| |       \__, \__/ |  \ |___     [0;32m\`-._,-`-,[0m
                                        [0;32m`._,._,'[0m
[0;37m      ____[0m
[0;37m    .´ _  `.[0m
[0;37m   /  [0;32m|\[0m`-_ \[0m     [0;34m __        __   ___     [0m
[0;37m  |   [0;32m| \[0m  `-|[0m    [0;34m|__`  /\  |__) |__  |__/[0m
[0;37m   \ [0;32m|   \[0m  /[0m     [0;34m.__| /¯¯\ |  \ |___ |  \[0m
[0;37m    `[0;32m|[0m____[0;32m\[0m´[0m

[0;35m  nf-core/sarek v3.2.3[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
  [0;34mrunName              : [0;32mberserk_yonath[0m
  [0;34mcontainerEngine      : [0;32mdocker[0m
  [0;34mlaunchDir            : [0;32m/TEST[0m
  [0;34mworkDir              : [0;32m/TEST/work[0m
  [0;34mprojectDir           : [0;32m/TEST/sarek[0m
  [0;34muserName             : [0;32mjgs8049[0m
  [0;34mprofile              : [0;32mdocker[0m
  [0;34mconfigFiles          : [0;32m/TEST/sarek/nextflow.config, /TEST/my_config.config[0m

[1mInput/output options[0m
  [0;34minput                : [0;32m/TEST/samplesheet.csv[0m
  [0;34moutdir               : [0;32m/TEST/results/[0m

[1mMain options[0m
  [0;34mintervals            : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed[0m

[1mVariant Calling[0m
  [0;34mcf_chrom_len         : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len[0m
  [0;34mpon                  : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz[0m
  [0;34mpon_tbi              : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi[0m

[1mReference genome options[0m
  [0;34mascat_genome         : [0;32mhg38[0m
  [0;34mascat_alleles        : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip[0m
  [0;34mascat_loci           : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip[0m
  [0;34mascat_loci_gc        : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip[0m
  [0;34mascat_loci_rt        : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip[0m
  [0;34mbwa                  : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/[0m
  [0;34mbwamem2              : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/[0m
  [0;34mchr_dir              : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes[0m
  [0;34mdbsnp                : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz[0m
  [0;34mdbsnp_tbi            : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi[0m
  [0;34mdbsnp_vqsr           : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m
  [0;34mdict                 : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict[0m
  [0;34mdragmap              : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/[0m
  [0;34mfasta                : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta[0m
  [0;34mfasta_fai            : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai[0m
  [0;34mgermline_resource    : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz[0m
  [0;34mgermline_resource_tbi: [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi[0m
  [0;34mknown_indels         : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz[0m
  [0;34mknown_indels_tbi     : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi[0m
  [0;34mknown_indels_vqsr    : [0;32m--resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz[0m
  [0;34mknown_snps           : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz[0m
  [0;34mknown_snps_tbi       : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi[0m
  [0;34mknown_snps_vqsr      : [0;32m--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz[0m
  [0;34mmappability          : [0;32ms3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem[0m
  [0;34msnpeff_db            : [0;32m105[0m
  [0;34msnpeff_genome        : [0;32mGRCh38[0m
  [0;34msnpeff_version       : [0;32m5.1[0m
  [0;34mvep_genome           : [0;32mGRCh38[0m
  [0;34mvep_species          : [0;32mhomo_sapiens[0m
  [0;34mvep_cache_version    : [0;32m108[0m
  [0;34mvep_version          : [0;32m108.2[0m
  [0;34migenomes_base        : [0;32ms3://ngi-igenomes/igenomes[0m

[1mMax job request options[0m
  [0;34mmax_cpus             : [0;32m8[0m
  [0;34mmax_memory           : [0;32m120 GB[0m
  [0;34mmax_time             : [0;32m72.h[0m

!! Only displaying parameters that differ from the pipeline defaults !!
Displaying all reference genome parameters
-[2m----------------------------------------------------[0m-
If you use nf-core/sarek for your analysis please cite:

* The pipeline
  https://doi.org/10.12688/f1000research.16665.2
  https://doi.org/10.5281/zenodo.4468605

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/sarek/blob/master/CITATIONS.md
-[2m----------------------------------------------------[0m-
Jul-28 07:33:01.993 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 1.16.2
Jul-28 07:33:02.022 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@1.16.2' resolved
Jul-28 07:33:02.022 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@1.16.2'
Jul-28 07:33:02.048 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@1.16.2
Jul-28 07:33:02.070 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3]
Jul-28 07:33:02.070 [main] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
Jul-28 07:33:02.084 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider
Jul-28 07:33:02.094 [main] DEBUG nextflow.Global - Using AWS credential defined in `default` section in file: /.aws/credentials
Jul-28 07:33:02.096 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {secret_key=JYDgz1.., region=us-east-1, max_error_retry=5, access_key=AKIAVI..}
Jul-28 07:33:02.420 [main] DEBUG com.upplication.s3fs.AmazonS3Client - Setting S3 glacierRetrievalTier=null
Jul-28 07:33:22.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jul-28 07:33:22.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jul-28 07:33:22.495 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.496 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.505 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
Jul-28 07:33:22.508 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m 
Jul-28 07:33:22.511 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Jul-28 07:33:22.568 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jul-28 07:33:22.568 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jul-28 07:33:22.571 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.571 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.576 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jul-28 07:33:22.576 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jul-28 07:33:22.578 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.578 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.582 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jul-28 07:33:22.583 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jul-28 07:33:22.585 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.585 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.590 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jul-28 07:33:22.590 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jul-28 07:33:22.592 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.592 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.597 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jul-28 07:33:22.597 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jul-28 07:33:22.600 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.600 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.610 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jul-28 07:33:22.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jul-28 07:33:22.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jul-28 07:33:22.612 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jul-28 07:33:22.614 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.614 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jul-28 07:33:22.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jul-28 07:33:22.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jul-28 07:33:22.620 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jul-28 07:33:22.622 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.622 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.626 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jul-28 07:33:22.627 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jul-28 07:33:22.627 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jul-28 07:33:22.627 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jul-28 07:33:22.629 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.629 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.633 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jul-28 07:33:22.633 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jul-28 07:33:22.634 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jul-28 07:33:22.634 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jul-28 07:33:22.636 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.636 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jul-28 07:33:22.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jul-28 07:33:22.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jul-28 07:33:22.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jul-28 07:33:22.642 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.642 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.646 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES
Jul-28 07:33:22.646 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES
Jul-28 07:33:22.647 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES
Jul-28 07:33:22.647 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES
Jul-28 07:33:22.649 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.649 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.655 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI
Jul-28 07:33:22.656 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI
Jul-28 07:33:22.657 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI
Jul-28 07:33:22.657 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI
Jul-28 07:33:22.659 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.659 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC
Jul-28 07:33:22.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC
Jul-28 07:33:22.665 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC
Jul-28 07:33:22.665 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC
Jul-28 07:33:22.667 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.667 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.672 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT
Jul-28 07:33:22.672 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT
Jul-28 07:33:22.673 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT
Jul-28 07:33:22.674 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT
Jul-28 07:33:22.676 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.676 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.726 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jul-28 07:33:22.726 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jul-28 07:33:22.731 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.731 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.770 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jul-28 07:33:22.771 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jul-28 07:33:22.772 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jul-28 07:33:22.773 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jul-28 07:33:22.777 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.777 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jul-28 07:33:22.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jul-28 07:33:22.787 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jul-28 07:33:22.790 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.790 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.807 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jul-28 07:33:22.808 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jul-28 07:33:22.809 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.809 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.814 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jul-28 07:33:22.814 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jul-28 07:33:22.816 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.816 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.820 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jul-28 07:33:22.821 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jul-28 07:33:22.823 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.823 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.827 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jul-28 07:33:22.828 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jul-28 07:33:22.829 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.829 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.842 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jul-28 07:33:22.843 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jul-28 07:33:22.845 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.845 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jul-28 07:33:22.851 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jul-28 07:33:22.852 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.852 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.856 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jul-28 07:33:22.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jul-28 07:33:22.859 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.859 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.865 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jul-28 07:33:22.866 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jul-28 07:33:22.867 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.867 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC
Jul-28 07:33:22.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC
Jul-28 07:33:22.883 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.883 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.891 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP
Jul-28 07:33:22.891 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP
Jul-28 07:33:22.893 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.893 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.907 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jul-28 07:33:22.907 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jul-28 07:33:22.907 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jul-28 07:33:22.908 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jul-28 07:33:22.908 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jul-28 07:33:22.909 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.909 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jul-28 07:33:22.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jul-28 07:33:22.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jul-28 07:33:22.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jul-28 07:33:22.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jul-28 07:33:22.915 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.915 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jul-28 07:33:22.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jul-28 07:33:22.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jul-28 07:33:22.922 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.922 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.939 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jul-28 07:33:22.939 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jul-28 07:33:22.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jul-28 07:33:22.941 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.941 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.949 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jul-28 07:33:22.949 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jul-28 07:33:22.950 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.950 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
Jul-28 07:33:22.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
Jul-28 07:33:22.965 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.965 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:22.985 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jul-28 07:33:22.986 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jul-28 07:33:22.986 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jul-28 07:33:22.986 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jul-28 07:33:22.988 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:22.988 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jul-28 07:33:23.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jul-28 07:33:23.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jul-28 07:33:23.015 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.015 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jul-28 07:33:23.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jul-28 07:33:23.023 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jul-28 07:33:23.024 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.024 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jul-28 07:33:23.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jul-28 07:33:23.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jul-28 07:33:23.047 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.047 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.058 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
Jul-28 07:33:23.059 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
Jul-28 07:33:23.060 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.060 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.066 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jul-28 07:33:23.067 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jul-28 07:33:23.067 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jul-28 07:33:23.068 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.068 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.086 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
Jul-28 07:33:23.086 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
Jul-28 07:33:23.087 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.087 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.096 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
Jul-28 07:33:23.096 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
Jul-28 07:33:23.097 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
Jul-28 07:33:23.098 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.098 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.114 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jul-28 07:33:23.115 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jul-28 07:33:23.115 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM_RECAL` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jul-28 07:33:23.116 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.116 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.141 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-28 07:33:23.141 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-28 07:33:23.141 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-28 07:33:23.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.143 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC
Jul-28 07:33:23.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC
Jul-28 07:33:23.227 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jul-28 07:33:23.227 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jul-28 07:33:23.235 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKEGRAPH, CONTROLFREEC_MAKEGRAPH, SAMTOOLS_VIEW_MAP_MAP, SVDB_MERGE, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS, MERGE_GENOTYPEGVCFS, SAMTOOLS_MERGE, BWA_MEM, GATK4_APPLYBQSR_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE, FILTERVARIANTTRANCHES, BUILD_INTERVALS, ADD_INFO_TO_VCF, SAMTOOLS_VIEW_UNMAP_UNMAP, CAT_FASTQ, CONTROLFREEC_FREEC2CIRCOS, SAMTOOLS_STATS, INDEX_MERGE_BAM, MUTECT2, GATK4_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR, TABIX_EXT_VCF, VCFTOOLS, NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX, TABIX_TABIX, FASTQC, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM, MULTIQC, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY, TABIX_GERMLINE_RESOURCE, ASSESS_SIGNIFICANCE, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT, CALLUMICONSENSUS, TABIX_KNOWN_SNPS, CAT_CAT, NFCORE_SAREK:SAREK:FASTQC, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON, GATHERPILEUPSUMMARIES_NORMAL, SAMTOOLS_FAIDX, MERGE_BAM, STRELKA_GERMLINE, TIDDIT_SV, GETPILEUPSUMMARIES_TUMOR, STRELKA_SINGLE, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES, SAMTOOLS_BAM2FQ, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP, BWAMEM2_MEM, VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE, UNZIP_ALLELES, GATK4_GETPILEUPSUMMARIES, BCFTOOLS_STATS, LEARNREADORIENTATIONMODEL, GATK4_VARIANTRECALIBRATOR, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS, FASTP, NFCORE_SAREK:SAREK:CRAM_TO_BAM, MERGE_FREEBAYES, MSISENSORPRO_SCAN, GATK4_MERGEVCFS, GATHERPILEUPSUMMARIES_TUMOR, UNTAR, TABIX_BGZIPTABIX_INTERVAL_SPLIT, MERGE_DEEPVARIANT_VCF, CNVKIT_REFERENCE, ENSEMBLVEP_VEP, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC, FREEC2BED, UNZIP_LOCI, TABIX_KNOWN_INDELS, GATK4_FILTERVARIANTTRANCHES, SNPEFF_SNPEFF, CREATE_INTERVALS_BED, BAM_TO_CRAM, GROUPREADSBYUMI, NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN, BAM_TO_CRAM_MAPPING, FASTQTOBAM, CONTROLFREEC_FREEC, NFCORE_SAREK:SAREK:MULTIQC, GATK4_ESTIMATELIBRARYCOMPLEXITY, BWAMEM1_MEM, CRAM_TO_BAM, GATK4_APPLYVQSR_SNP, GATK4_APPLYBQSR, GATK4_BASERECALIBRATOR, VCFTOOLS_TSTV_QUAL, GERMLINE_VCFS_CONCAT, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM, NFCORE_SAREK:SAREK:FASTP, TABIX_DBSNP, FILTERMUTECTCALLS, CNNSCOREVARIANTS, SNPEFF_DOWNLOAD, MANTA_GERMLINE, GATK4_LEARNREADORIENTATIONMODEL, BWA_INDEX, INDEX_MARKDUPLICATES, MERGE_HAPLOTYPECALLER, GERMLINE_VCFS_CONCAT_SORT, STRELKA_SOMATIC, FREEC_SOMATIC, GATK4_MUTECT2, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR, VARIANTRECALIBRATOR_INDEL, MERGE_BCFTOOLS_MPILEUP, CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM, FGBIO_FASTQTOBAM, CRAM_TO_BAM_RECAL, ENSEMBLVEP_DOWNLOAD, GATK4_GATHERBQSRREPORTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT, TABIX_BGZIPTABIX, GATK4_MARKDUPLICATES_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES, GATK4_CREATESEQUENCEDICTIONARY, CALCULATECONTAMINATION, MERGE_DEEPVARIANT_GVCF, COLLATE_FASTQ_MAP, TABIX_VC_FREEBAYES, MOSDEPTH, MERGE_STRELKA_INDELS, UNZIP, COLLATE_FASTQ_UNMAP, UNZIP_GC, VCFTOOLS_TSTV_COUNT, GATK4_MERGEMUTECTSTATS, CAT_MPILEUP, CONTROLFREEC_ASSESSSIGNIFICANCE, MANTA_TUMORONLY, BWAMEM2_INDEX, MERGE_STRELKA_SNVS, SAMTOOLS_VIEW_MAP_UNMAP, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI, MERGE_STRELKA, BCFTOOLS_CONCAT, SAMTOOLS_INDEX, MERGE_CRAM, GATK4_CNNSCOREVARIANTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP, TABIX_BGZIP_TIDDIT_SV, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED, TABIX_PON, VARIANTRECALIBRATOR_SNP, TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS, UNTAR_CHR_DIR, FREEC_TUMORONLY, SAMBLASTER, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH, FREEBAYES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP, GATHERPILEUPSUMMARIES, NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL, SAMTOOLS_MPILEUP, INDEX_CRAM, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ, BCFTOOLS_SORT, MANTA_SOMATIC, NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS, GATK4_FILTERMUTECTCALLS, MERGE_VQSR, MUTECT2_PAIRED, BWAMEM1_INDEX, GATK4_GATHERPILEUPSUMMARIES, DRAGMAP_HASHTABLE, CNVKIT_ANTITARGET, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN, GATK4_MARKDUPLICATES, SAMTOOLS_VIEW_UNMAP_MAP, SAMTOOLS_CONVERT, TABIX_GERMLINE_VCFS_CONCAT_SORT, CONTROLFREEC_FREEC2BED, MERGE_STRELKA_GENOME, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP, BAM2FASTQ, UNZIP_RT, MERGEMUTECTSTATS, SAMTOOLS_COLLATEFASTQ, GATK4_APPLYVQSR, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM, GATK4_CALCULATECONTAMINATION, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS, DEEPVARIANT, GATK4_GENOTYPEGVCFS, MSISENSORPRO_MSI_SOMATIC, FREEC2CIRCOS, DRAGMAP_ALIGN, GATK4_INTERVALLISTTOBED, GATK4_APPLYVQSR_INDEL, FGBIO_GROUPREADSBYUMI, BCFTOOLS_MPILEUP, SAMTOOLS_VIEW, CNVKIT_BATCH, GETPILEUPSUMMARIES, FGBIO_CALLMOLECULARCONSENSUSREADS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP, GETPILEUPSUMMARIES_NORMAL, GATK4_GENOMICSDBIMPORT, MERGE_MUTECT2, GATK4_BASERECALIBRATOR_SPARK, ASCAT
Jul-28 07:33:23.275 [main] WARN  nextflow.Session - There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS?
Jul-28 07:33:23.278 [main] DEBUG nextflow.Session - Igniting dataflow network (118)
Jul-28 07:33:23.293 [PathVisitor-4] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz; options: [:]
Jul-28 07:33:23.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jul-28 07:33:23.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jul-28 07:33:23.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jul-28 07:33:23.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC
Jul-28 07:33:23.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT
Jul-28 07:33:23.314 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi; options: [:]
Jul-28 07:33:23.319 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jul-28 07:33:23.320 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jul-28 07:33:23.327 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jul-28 07:33:23.327 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jul-28 07:33:23.327 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
Jul-28 07:33:23.352 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jul-28 07:33:23.396 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jul-28 07:33:23.396 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jul-28 07:33:23.396 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jul-28 07:33:23.397 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
Jul-28 07:33:23.397 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jul-28 07:33:23.397 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
Jul-28 07:33:23.397 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
Jul-28 07:33:23.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jul-28 07:33:23.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-28 07:33:23.400 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC
Jul-28 07:33:23.400 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jul-28 07:33:23.400 [main] DEBUG nextflow.Session - Session await
Jul-28 07:33:23.520 [Actor Thread 6] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.016 s; total time: 0.018 s
Jul-28 07:33:23.520 [Actor Thread 50] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.016 s; total time: 0.018 s
Jul-28 07:33:23.542 [Actor Thread 50] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /TEST/work/collect-file/958119e01f38c6515e719c469b8de10b
Jul-28 07:33:23.545 [Actor Thread 6] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /TEST/work/collect-file/271f11d1d58b5837de013c0338aaeba9
Jul-28 07:33:23.551 [Actor Thread 6] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6061139647973115043
Jul-28 07:33:23.551 [Actor Thread 50] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-981208115256002952
Jul-28 07:33:23.696 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1) > jobId: 2492; workDir: /TEST/work/1d/924701c52e4b085b27acff4499e4c6
Jul-28 07:33:23.697 [Task submitter] INFO  nextflow.Session - [1d/924701] Submitted process > NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)
Jul-28 07:33:23.746 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1) > jobId: 2493; workDir: /TEST/work/1f/c0e005e27cd67b033671dfbb4f720f
Jul-28 07:33:23.746 [Task submitter] INFO  nextflow.Session - [1f/c0e005] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)
Jul-28 07:33:25.379 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/0d/3ffa114a62c5d4383e933d2692a8e0/Homo_sapiens_assembly38.fasta
Jul-28 07:33:25.379 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/6d/51871f94e9666ad5741b937898e857/G1000_alleles_hg38.zip
Jul-28 07:33:25.380 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/dc/bd55318c3bd0b043bf425da6b0b8b6/wgs_calling_regions_noseconds.hg38.bed
Jul-28 07:33:25.382 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/e4/db9b64c6025394285081282396d88f/1000G_omni2.5.hg38.vcf.gz
Jul-28 07:33:25.383 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/e4/1da12f51d30899fe7de411f8c28d93/RT_G1000_hg38.zip
Jul-28 07:33:25.383 [FileTransfer-6] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/99/bb16aad07f0498f99c5e5619c12dbc/GC_G1000_hg38.zip
Jul-28 07:33:25.384 [FileTransfer-7] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/58/de7e64e53777b8ad5ea8b37b164f31/1000g_pon.hg38.vcf.gz
Jul-28 07:33:25.473 [FileTransfer-2] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/6d/51871f94e9666ad5741b937898e857/G1000_alleles_hg38.zip
Jul-28 07:33:25.473 [FileTransfer-3] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/dc/bd55318c3bd0b043bf425da6b0b8b6/wgs_calling_regions_noseconds.hg38.bed
Jul-28 07:33:25.473 [FileTransfer-2] DEBUG com.upplication.s3fs.AmazonS3Client - Creating S3 transfer manager pool - chunk-size=104857600; max-treads=10;
Jul-28 07:33:25.473 [FileTransfer-2] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'S3TransferManager' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-28 07:33:25.473 [FileTransfer-1] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/0d/3ffa114a62c5d4383e933d2692a8e0/Homo_sapiens_assembly38.fasta
Jul-28 07:33:25.567 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.567 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.568 [Actor Thread 13] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (1); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXNN8ZM2JWC1FWC; S3 Extended Request ID: N+EAlbjfA3YU4RLLnD19QVv6UOiMRN6Y0TvG+CL8ZLnQIgFyeY2U0nkieRWSERpqwbcktRQHoWo=; Proxy: null)
Jul-28 07:33:25.567 [Actor Thread 35] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.567 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.567 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.568 [Actor Thread 48] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMJG1TE12D2N32; S3 Extended Request ID: 6BdFt6nhoHvGZxHCLETYYMlkCydsEiZ6yyrVO3fEGaSi5nksMdrMwoBgh7Blp66h96iu/4VSLho=; Proxy: null)
Jul-28 07:33:25.572 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.572 [Actor Thread 23] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.572 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.572 [Actor Thread 17] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.572 [Actor Thread 25] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.572 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.576 [Actor Thread 35] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX'

Caused by:
  Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)

com.amazonaws.services.s3.model.AmazonS3Exception: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleErrorResponse(AmazonHttpClient.java:1879)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleServiceErrorResponse(AmazonHttpClient.java:1418)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1387)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1157)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:814)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:781)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:755)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:715)
    at com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:697)
    at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:561)
    at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:541)
    at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5456)
    at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5403)
    at com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1372)
    at com.amazonaws.services.s3.transfer.TransferManager.prepareDownload(TransferManager.java:1094)
    at com.amazonaws.services.s3.transfer.TransferManager.doDownload(TransferManager.java:1050)
    at com.amazonaws.services.s3.transfer.TransferManager.doDownload(TransferManager.java:1027)
    at com.amazonaws.services.s3.transfer.TransferManager.download(TransferManager.java:861)
    at com.amazonaws.services.s3.transfer.TransferManager.download(TransferManager.java:779)
    at com.amazonaws.services.s3.transfer.TransferManager.download(TransferManager.java:733)
    at com.upplication.s3fs.AmazonS3Client.downloadFile(AmazonS3Client.java:572)
    at com.upplication.s3fs.S3FileSystemProvider.download(S3FileSystemProvider.java:368)
    at nextflow.file.FileHelper.copyPath(FileHelper.groovy:964)
    at nextflow.file.FilePorter$FileTransfer.stageForeignFile0(FilePorter.groovy:324)
    at nextflow.file.FilePorter$FileTransfer.stageForeignFile(FilePorter.groovy:291)
    at nextflow.file.FilePorter$FileTransfer.run(FilePorter.groovy:277)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
Jul-28 07:33:25.579 [Actor Thread 35] DEBUG nextflow.Session - Session aborted -- Cause: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.597 [Actor Thread 35] DEBUG nextflow.Session - The following nodes are still active:
[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
  status=ACTIVE
  port 0: (value) bound ; channel: intervals
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: sort_bam
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: sort_bam
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: sort_bam
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: fasta
  port 2: (value) bound ; channel: fasta_fai
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:CRAM_TO_BAM
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: fasta
  port 2: (value) bound ; channel: fai
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: fasta
  port 2: (value) bound ; channel: fai
  port 3: (value) bound ; channel: dict
  port 4: (value) bound ; channel: known_sites
  port 5: (value) bound ; channel: known_sites_tbi
  port 6: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: fasta
  port 2: (value) bound ; channel: fai
  port 3: (value) bound ; channel: dict
  port 4: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: fasta
  port 2: (value) bound ; channel: fai
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: versions
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_SAREK:SAREK:MULTIQC
  status=ACTIVE
  port 0: (value) OPEN  ; channel: multiqc_files
  port 1: (value) bound ; channel: multiqc_config
  port 2: (value) bound ; channel: extra_multiqc_config
  port 3: (value) bound ; channel: multiqc_logo
  port 4: (cntrl) -     ; channel: $

Jul-28 07:33:25.599 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-28 07:33:25.599 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-28 07:33:25.600 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.600 [Actor Thread 22] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.600 [Actor Thread 52] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.600 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.600 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.600 [Actor Thread 24] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.600 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.601 [Actor Thread 11] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.601 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.601 [main] INFO  nextflow.Nextflow - -[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m-
Jul-28 07:33:25.602 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.603 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.604 [Actor Thread 18] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-28 07:33:25.604 [Actor Thread 5] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-28 07:33:25.605 [Actor Thread 7] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-28 07:33:25.605 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-28 07:33:25.606 [Actor Thread 52] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-28 07:33:25.606 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (2)
Jul-28 07:33:25.639 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=2; runningCount=-2; retriesCount=0; abortedCount=2; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=-12; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Jul-28 07:33:25.639 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-28 07:33:25.641 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-28 07:33:25.658 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"FASTP","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null},{"cpuUsage":null,"process":"FASTQC","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}]
Jul-28 07:33:25.695 [FileTransfer-6] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/99/bb16aad07f0498f99c5e5619c12dbc/GC_G1000_hg38.zip
Jul-28 07:33:25.701 [FileTransfer-7] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/58/de7e64e53777b8ad5ea8b37b164f31/1000g_pon.hg38.vcf.gz
Jul-28 07:33:25.772 [Actor Thread 16] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXP2CEZXTHWMRQW; S3 Extended Request ID: Blo+9bkw3kNWQYIhRHBMiXv3ubiybGMxgp0+Dgn7tcIMYjASX4qIsTRj24+cc44XNU5GbgKKIPU=; Proxy: null)
Jul-28 07:33:25.780 [Actor Thread 49] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON (1); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMAX34C3J4DQ7F; S3 Extended Request ID: P00Ujc1saU3Vl19qTclLiCn6TQWPAwGn/i4mcewpviYRvwP74k3urlJjPT4vzR0EjU6kc8M49kE=; Proxy: null)
Jul-28 07:33:25.795 [FileTransfer-4] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/e4/db9b64c6025394285081282396d88f/1000G_omni2.5.hg38.vcf.gz
Jul-28 07:33:25.795 [FileTransfer-5] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/e4/1da12f51d30899fe7de411f8c28d93/RT_G1000_hg38.zip
Jul-28 07:33:25.816 [FileTransfer-8] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/f4/6bdd4766de096b18958db2caa77e4f/af-only-gnomad.hg38.vcf.gz
Jul-28 07:33:25.817 [Actor Thread 45] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXNN8ZM2JWC1FWC; S3 Extended Request ID: N+EAlbjfA3YU4RLLnD19QVv6UOiMRN6Y0TvG+CL8ZLnQIgFyeY2U0nkieRWSERpqwbcktRQHoWo=; Proxy: null)
Jul-28 07:33:25.817 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXMTYBKMQKEVVXR; S3 Extended Request ID: FwyokOQPfHZ488HMGVUsArRjy5K2i2XnwuEamXZePa7TOqyv2Qbps3oQCaJOH2wJ31ys03l4n64=; Proxy: null)
Jul-28 07:33:25.818 [FileTransfer-9] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/36/795c6971d037869be2acff9c56d4e3/G1000_loci_hg38.zip
Jul-28 07:33:25.818 [FileTransfer-10] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/01/be706f4d882eb6b64ebeb99e5ef543/Homo_sapiens_assembly38.known_indels.vcf.gz
Jul-28 07:33:25.818 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/5c/6f80c5ca518a0c6de51c3dab1b487f/dbsnp_146.hg38.vcf.gz
Jul-28 07:33:25.818 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz to work dir: /TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/b2/9ae238800d40eee44fbdb1a7506396/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
Jul-28 07:33:25.873 [Actor Thread 44] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS (1); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXWAR2T4J7FXKY2; S3 Extended Request ID: lpffejAKrCH0VBb4uieE1f40ch8cPMecG5Mz7fo2WZTu2iNdJxSScOlnNPi+oOkwLe8TCAuiDOc=; Proxy: null)
Jul-28 07:33:25.874 [Actor Thread 42] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXYS6B65ADEYBFY; S3 Extended Request ID: kWjMfCHSyPpQ2bDMHFtYbI8NvaCtuuwJnF3giMP91s9ADk3beEgsfTJtvfvoF4Xp4FEJpKaJ+D0=; Proxy: null)
Jul-28 07:33:25.909 [FileTransfer-9] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/36/795c6971d037869be2acff9c56d4e3/G1000_loci_hg38.zip
Jul-28 07:33:25.909 [FileTransfer-3] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/5c/6f80c5ca518a0c6de51c3dab1b487f/dbsnp_146.hg38.vcf.gz
Jul-28 07:33:25.909 [FileTransfer-1] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/b2/9ae238800d40eee44fbdb1a7506396/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
Jul-28 07:33:25.910 [FileTransfer-10] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/01/be706f4d882eb6b64ebeb99e5ef543/Homo_sapiens_assembly38.known_indels.vcf.gz
Jul-28 07:33:25.912 [FileTransfer-8] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz to=/TEST/work/stage-43d5f3c7-a484-4b55-94a9-cb55beaee6d6/f4/6bdd4766de096b18958db2caa77e4f/af-only-gnomad.hg38.vcf.gz
Jul-28 07:33:25.987 [Actor Thread 38] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP (1); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXY0VYCJJ4VQ5DK; S3 Extended Request ID: rlD7V23Dz2n3Pag08aQedmt45q2OqWcJkIOEeueNA+XJTt86ezFeB8uEjPLu3lAwMWFNp4F/j3o=; Proxy: null)
Jul-28 07:33:25.987 [Actor Thread 50] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS (1); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXYVTTJV3HWH515; S3 Extended Request ID: 0SdxlBMrlClfzj42slr23Hopsq/RDnzNet8BMojTYZNwefk1oVTTNZrP0elZelHx7S9uy6jypCQ=; Proxy: null)
Jul-28 07:33:25.988 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI; work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXXE2JPGFTDCMBE; S3 Extended Request ID: 5y8nbl/t9DWTwv4Nn+Wt7BdzgkGrUD+Dmta+4BFkVvIp17m4ME093TTdCoIdt+B6CLC9N3SLmmE=; Proxy: null)
Jul-28 07:33:25.990 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE (1); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXJHNDCJFH0JWJV; S3 Extended Request ID: PjeKvmGND0+g4Cvo3ts/W/3MN/2mjRMJ3Qra6iOuKVOAixy6D5oXcSQhEprnmsWbIkg49KYfNDY=; Proxy: null)
Jul-28 07:33:25.991 [Actor Thread 43] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS (2); work-dir=null
  error [com.amazonaws.services.s3.model.AmazonS3Exception]: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: 6SXH5AQ25EK9D6CW; S3 Extended Request ID: 7sXFSuYQ2lsbtdTvRSxaw7nOakIHvbZDHKZBQ1sM5utuhaw1cpGdsIIon8Lsu5CES73IcU1OV3c=; Proxy: null)
Jul-28 07:33:26.311 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-28 07:33:26.477 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-28 07:33:26.477 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@1.16.2'
Jul-28 07:33:26.477 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon
Jul-28 07:33:26.551 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

######################### Can you please help.

#SBATCH --job-name=cd_301 #SBATCH --nodes=1 #SBATCH --tasks=2 #SBATCH --cpus-per-task=8 #SBATCH --tasks-per-node=1 #SBATCH --output=/sarek_301_%j.out #SBATCH --chdir=/TEST/ #SBATCH --error=/TEST/sarek_300_%j.err #aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/ ./references/Homo_sapiens/GATK/GRCh38/ nextflow run nf-core/sarek -r 3.2.1 -c my_config.config -profile docker --input /TEST/samplesheet.csv --genome GATK.GRCh38 --igenomes_base '/TEST/references' --outdir /TEST/results/ --max_cpus 8

Aug-07 09:45:13.719 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -r 3.2.1 -c my_config.config -profile docker --input /TEST/samplesheet.csv --genome GATK.GRCh38 --igenomes_base /TEST/references --outdir /TEST/results/ --max_cpus 8 Aug-07 09:45:13.901 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2 Aug-07 09:45:13.920 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3 Aug-07 09:45:13.938 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Aug-07 09:45:13.940 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Aug-07 09:45:13.944 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Aug-07 09:45:13.954 [main] INFO org.pf4j.AbstractPluginManager - No plugins Aug-07 09:45:13.973 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /.nextflow/scm Aug-07 09:45:15.170 [main] DEBUG nextflow.scm.AssetManager - Git config: /.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git Aug-07 09:45:15.195 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Aug-07 09:45:15.209 [main] DEBUG nextflow.scm.AssetManager - Git config: /.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git Aug-07 09:45:16.071 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /.nextflow/assets/nf-core/sarek/nextflow.config Aug-07 09:45:16.075 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /TEST/my_config.config Aug-07 09:45:16.076 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /.nextflow/assets/nf-core/sarek/nextflow.config Aug-07 09:45:16.076 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /TEST/my_config.config Aug-07 09:45:16.086 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker` Aug-07 09:45:18.716 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker` Aug-07 09:45:18.741 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, uge, rosalind_uge, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, public_aws_ecr, tigem, tubingen_apg, google, ipop_up, googlels, use_gatk_spark, eddie, medair, alignment_to_fastq, biowulf, apptainer, bi, bigpurple, sbc_sharc, adcra, cedars, tools, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, targeted, icr_davros, ceres, save_bam_mapped, munin, arm, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, wustl_htcf, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, ebi_codon, cheaha, xanadu, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, dkfz, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, hypatia, psmn, umi, eva, markduplicates_bam, fgcz, conda, crg, singularity, uw_hyak_pedslabs, prince, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, seawulf, fub_curta, uct_hpc, aws_tower, binac] Aug-07 09:45:18.786 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Aug-07 09:45:18.787 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [sleepy_fourier] DSL2 - revision: 6c0d335e17 [3.2.1] Aug-07 09:45:18.788 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Aug-07 09:45:18.788 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Aug-07 09:45:18.791 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /.nextflow/secrets/store.json Aug-07 09:45:18.794 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@174f0d06] - activable => nextflow.secret.LocalSecretsProvider@174f0d06 Aug-07 09:45:18.856 [main] DEBUG nextflow.Session - Session UUID: e0e4c7c0-9bda-4e57-a84a-38e4c17978eb Aug-07 09:45:18.856 [main] DEBUG nextflow.Session - Run name: sleepy_fourier Aug-07 09:45:18.856 [main] DEBUG nextflow.Session - Executor pool size: 8 Aug-07 09:45:18.866 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Aug-07 09:45:18.887 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.2 build 5870 Created: 08-06-2023 08:29 UTC System: Linux 5.10.144-127.601.amzn2.x86_64 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.7+7-LTS Encoding: UTF-8 (UTF-8) Process: 26535@queue1-st-r54xlarge-1 [10.70.135.98] CPUs: 8 - Mem: 124.4 GB (54.1 GB) - Swap: 24 GB (19.4 GB) Aug-07 09:45:18.944 [main] DEBUG nextflow.Session - Work-dir: /TEST/work [nfs] Aug-07 09:45:18.945 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /.nextflow/assets/nf-core/sarek/bin Aug-07 09:45:18.955 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Aug-07 09:45:18.965 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Aug-07 09:45:19.068 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Aug-07 09:45:19.077 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Aug-07 09:45:19.303 [main] DEBUG nextflow.Session - Session start Aug-07 09:45:19.307 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /TEST/results/pipeline_info/execution_trace_2023-08-07_09-45-17.txt Aug-07 09:45:19.326 [main] DEBUG nextflow.Session - Using default localLib path: /.nextflow/assets/nf-core/sarek/lib Aug-07 09:45:19.332 [main] DEBUG nextflow.Session - Adding to the classpath library: /.nextflow/assets/nf-core/sarek/lib Aug-07 09:45:19.333 [main] DEBUG nextflow.Session - Adding to the classpath library: /.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar Aug-07 09:45:20.368 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Aug-07 09:45:20.439 [main] INFO nextflow.Nextflow - -[2m----------------------------------------------------[0m- [0;32m,--.[0;30m/[0;32m,-.[0m [0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m [0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m [0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m [0;32m`._,._,'[0m [0;37m ____[0m [0;37m .´ _ `.[0m [0;37m / [0;32m|\[0m`-_ \[0m [0;34m __ __ ___ [0m [0;37m | [0;32m| \[0m `-|[0m [0;34m|__` /\ |__) |__ |__/[0m [0;37m \ [0;32m| \[0m /[0m [0;34m.__| /¯¯\ | \ |___ | \[0m [0;37m `[0;32m|[0m____[0;32m\[0m´[0m [0;35m nf-core/sarek v3.2.1-g6c0d335[0m -[2m----------------------------------------------------[0m- [1mCore Nextflow options[0m [0;34mrevision : [0;32m3.2.1[0m [0;34mrunName : [0;32msleepy_fourier[0m [0;34mcontainerEngine : [0;32mdocker[0m [0;34mlaunchDir : [0;32m/TEST[0m [0;34mworkDir : [0;32m/TEST/work[0m [0;34mprojectDir : [0;32m/.nextflow/assets/nf-core/sarek[0m [0;34muserName : [0;32mjgs8049[0m [0;34mprofile : [0;32mdocker[0m [0;34mconfigFiles : [0;32m/.nextflow/assets/nf-core/sarek/nextflow.config, /TEST/my_config.config[0m [1mInput/output options[0m [0;34minput : [0;32m/TEST/samplesheet.csv[0m [0;34moutdir : [0;32m/TEST/results/[0m [1mMain options[0m [0;34mintervals : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed[0m [1mVariant Calling[0m [0;34mcf_chrom_len : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len[0m [0;34mpon : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz[0m [0;34mpon_tbi : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi[0m [1mReference genome options[0m [0;34mascat_genome : [0;32mhg38[0m [0;34mascat_alleles : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip[0m [0;34mascat_loci : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip[0m [0;34mascat_loci_gc : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip[0m [0;34mascat_loci_rt : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip[0m [0;34mbwa : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/[0m [0;34mbwamem2 : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/[0m [0;34mchr_dir : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes[0m [0;34mdbsnp : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz[0m [0;34mdbsnp_tbi : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi[0m [0;34mdbsnp_vqsr : [0;32m--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz[0m [0;34mdict : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict[0m [0;34mdragmap : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/[0m [0;34mfasta : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta[0m [0;34mfasta_fai : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai[0m [0;34mgermline_resource : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz[0m [0;34mgermline_resource_tbi: [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi[0m [0;34mknown_indels : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz[0m [0;34mknown_indels_tbi : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi[0m [0;34mknown_indels_vqsr : [0;32m--resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz[0m [0;34mknown_snps : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz[0m [0;34mknown_snps_tbi : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi[0m [0;34mknown_snps_vqsr : [0;32m--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz[0m [0;34mmappability : [0;32m/TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem[0m [0;34msnpeff_db : [0;32m105[0m [0;34msnpeff_genome : [0;32mGRCh38[0m [0;34msnpeff_version : [0;32m5.1[0m [0;34mvep_genome : [0;32mGRCh38[0m [0;34mvep_species : [0;32mhomo_sapiens[0m [0;34mvep_cache_version : [0;32m108[0m [0;34mvep_version : [0;32m108.2[0m [0;34migenomes_base : [0;32m/TEST/references[0m [1mMax job request options[0m [0;34mmax_cpus : [0;32m8[0m [0;34mmax_memory : [0;32m120 GB[0m [0;34mmax_time : [0;32m72.h[0m !! Only displaying parameters that differ from the pipeline defaults !! Displaying all reference genome parameters -[2m----------------------------------------------------[0m- If you use nf-core/sarek for your analysis please cite: * The pipeline https://doi.org/10.12688/f1000research.16665.2 https://doi.org/10.5281/zenodo.4468605 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/sarek/blob/master/CITATIONS.md -[2m----------------------------------------------------[0m- Aug-07 09:45:44.312 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Aug-07 09:45:44.315 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Aug-07 09:45:44.322 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.322 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.331 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Aug-07 09:45:44.335 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Aug-07 09:45:44.337 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Aug-07 09:45:44.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Aug-07 09:45:44.392 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Aug-07 09:45:44.423 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.423 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.427 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Aug-07 09:45:44.432 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Aug-07 09:45:44.435 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.438 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.444 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Aug-07 09:45:44.445 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Aug-07 09:45:44.448 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.448 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.454 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Aug-07 09:45:44.454 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Aug-07 09:45:44.457 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.457 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.464 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Aug-07 09:45:44.464 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Aug-07 09:45:44.468 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.468 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.479 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Aug-07 09:45:44.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Aug-07 09:45:44.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Aug-07 09:45:44.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Aug-07 09:45:44.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.491 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Aug-07 09:45:44.491 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Aug-07 09:45:44.492 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Aug-07 09:45:44.492 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Aug-07 09:45:44.495 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.495 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Aug-07 09:45:44.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Aug-07 09:45:44.502 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Aug-07 09:45:44.503 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Aug-07 09:45:44.505 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.505 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Aug-07 09:45:44.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Aug-07 09:45:44.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Aug-07 09:45:44.512 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Aug-07 09:45:44.514 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.514 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Aug-07 09:45:44.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Aug-07 09:45:44.519 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Aug-07 09:45:44.519 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Aug-07 09:45:44.521 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.522 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.528 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Aug-07 09:45:44.528 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Aug-07 09:45:44.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Aug-07 09:45:44.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Aug-07 09:45:44.531 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.532 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.540 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Aug-07 09:45:44.540 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Aug-07 09:45:44.541 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Aug-07 09:45:44.541 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Aug-07 09:45:44.547 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.547 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Aug-07 09:45:44.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Aug-07 09:45:44.552 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Aug-07 09:45:44.552 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Aug-07 09:45:44.553 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.558 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Aug-07 09:45:44.558 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Aug-07 09:45:44.559 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Aug-07 09:45:44.559 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Aug-07 09:45:44.560 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.560 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.603 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Aug-07 09:45:44.603 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Aug-07 09:45:44.605 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.605 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.631 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Aug-07 09:45:44.631 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Aug-07 09:45:44.631 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Aug-07 09:45:44.632 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Aug-07 09:45:44.633 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.633 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Aug-07 09:45:44.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Aug-07 09:45:44.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Aug-07 09:45:44.641 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.641 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Aug-07 09:45:44.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Aug-07 09:45:44.666 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.666 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.670 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Aug-07 09:45:44.670 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Aug-07 09:45:44.672 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.672 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.675 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Aug-07 09:45:44.676 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Aug-07 09:45:44.677 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.677 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.681 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Aug-07 09:45:44.682 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Aug-07 09:45:44.683 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.683 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.703 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Aug-07 09:45:44.704 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Aug-07 09:45:44.705 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.705 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.717 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Aug-07 09:45:44.718 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Aug-07 09:45:44.719 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.719 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Aug-07 09:45:44.723 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Aug-07 09:45:44.724 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.724 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Aug-07 09:45:44.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Aug-07 09:45:44.734 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.734 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.752 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC Aug-07 09:45:44.752 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC Aug-07 09:45:44.753 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.754 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP Aug-07 09:45:44.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP Aug-07 09:45:44.762 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.762 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.778 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Aug-07 09:45:44.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Aug-07 09:45:44.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Aug-07 09:45:44.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Aug-07 09:45:44.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Aug-07 09:45:44.780 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.780 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Aug-07 09:45:44.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Aug-07 09:45:44.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Aug-07 09:45:44.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Aug-07 09:45:44.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Aug-07 09:45:44.790 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.790 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.794 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Aug-07 09:45:44.794 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Aug-07 09:45:44.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Aug-07 09:45:44.796 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.796 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.815 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Aug-07 09:45:44.815 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Aug-07 09:45:44.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Aug-07 09:45:44.817 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.817 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.821 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES Aug-07 09:45:44.821 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES Aug-07 09:45:44.822 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:INDEX_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES Aug-07 09:45:44.823 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.823 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.829 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Aug-07 09:45:44.829 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Aug-07 09:45:44.830 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.830 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH Aug-07 09:45:44.842 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH Aug-07 09:45:44.843 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.843 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM Aug-07 09:45:44.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Aug-07 09:45:44.860 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Aug-07 09:45:44.860 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Aug-07 09:45:44.861 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.861 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.884 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Aug-07 09:45:44.884 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Aug-07 09:45:44.885 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Aug-07 09:45:44.886 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.886 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Aug-07 09:45:44.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Aug-07 09:45:44.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Aug-07 09:45:44.893 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.893 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Aug-07 09:45:44.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Aug-07 09:45:44.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Aug-07 09:45:44.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM Aug-07 09:45:44.921 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM Aug-07 09:45:44.922 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.922 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.927 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Aug-07 09:45:44.927 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Aug-07 09:45:44.927 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Aug-07 09:45:44.928 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.928 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.941 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS Aug-07 09:45:44.942 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS Aug-07 09:45:44.943 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.943 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.950 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Aug-07 09:45:44.950 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Aug-07 09:45:44.950 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Aug-07 09:45:44.951 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.951 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Aug-07 09:45:44.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Aug-07 09:45:44.964 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM_RECAL` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Aug-07 09:45:44.964 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.964 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:44.989 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Aug-07 09:45:44.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Aug-07 09:45:44.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Aug-07 09:45:44.991 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:44.991 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:45.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC Aug-07 09:45:45.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC Aug-07 09:45:45.058 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Aug-07 09:45:45.058 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Aug-07 09:45:45.065 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKEGRAPH, CONTROLFREEC_MAKEGRAPH, SAMTOOLS_VIEW_MAP_MAP, SVDB_MERGE, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS, MERGE_GENOTYPEGVCFS, SAMTOOLS_MERGE, BWA_MEM, GATK4_APPLYBQSR_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE, ADD_INFO_TO_VCF, BUILD_INTERVALS, FILTERVARIANTTRANCHES, SAMTOOLS_VIEW_UNMAP_UNMAP, CAT_FASTQ, CONTROLFREEC_FREEC2CIRCOS, SAMTOOLS_STATS, INDEX_MERGE_BAM, MUTECT2, GATK4_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR, TABIX_EXT_VCF, VCFTOOLS, NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX, TABIX_TABIX, FASTQC, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM, MULTIQC, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY, TABIX_GERMLINE_RESOURCE, ASSESS_SIGNIFICANCE, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT, CALLUMICONSENSUS, TABIX_KNOWN_SNPS, CAT_CAT, NFCORE_SAREK:SAREK:FASTQC, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON, GATHERPILEUPSUMMARIES_NORMAL, SAMTOOLS_FAIDX, MERGE_BAM, STRELKA_GERMLINE, TIDDIT_SV, GETPILEUPSUMMARIES_TUMOR, STRELKA_SINGLE, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES, SAMTOOLS_BAM2FQ, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP, BWAMEM2_MEM, VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE, UNZIP_ALLELES, BCFTOOLS_STATS, GATK4_GETPILEUPSUMMARIES, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES, LEARNREADORIENTATIONMODEL, GATK4_VARIANTRECALIBRATOR, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS, FASTP, NFCORE_SAREK:SAREK:CRAM_TO_BAM, MERGE_FREEBAYES, MSISENSORPRO_SCAN, GATK4_MERGEVCFS, GATHERPILEUPSUMMARIES_TUMOR, TABIX_BGZIPTABIX_INTERVAL_SPLIT, UNTAR, MERGE_DEEPVARIANT_VCF, CNVKIT_REFERENCE, ENSEMBLVEP_VEP, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC, FREEC2BED, UNZIP_LOCI, GATK4_FILTERVARIANTTRANCHES, TABIX_KNOWN_INDELS, SNPEFF_SNPEFF, CREATE_INTERVALS_BED, BAM_TO_CRAM, GROUPREADSBYUMI, NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN, BAM_TO_CRAM_MAPPING, FASTQTOBAM, CONTROLFREEC_FREEC, NFCORE_SAREK:SAREK:MULTIQC, BWAMEM1_MEM, CRAM_TO_BAM, GATK4_ESTIMATELIBRARYCOMPLEXITY, GATK4_APPLYVQSR_SNP, GATK4_APPLYBQSR, GATK4_BASERECALIBRATOR, VCFTOOLS_TSTV_QUAL, GERMLINE_VCFS_CONCAT, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM, NFCORE_SAREK:SAREK:FASTP, TABIX_DBSNP, FILTERMUTECTCALLS, CNNSCOREVARIANTS, SNPEFF_DOWNLOAD, GATK4_LEARNREADORIENTATIONMODEL, BWA_INDEX, MANTA_GERMLINE, INDEX_MARKDUPLICATES, GERMLINE_VCFS_CONCAT_SORT, MERGE_HAPLOTYPECALLER, STRELKA_SOMATIC, FREEC_SOMATIC, GATK4_MUTECT2, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR, VARIANTRECALIBRATOR_INDEL, CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM, FGBIO_FASTQTOBAM, CRAM_TO_BAM_RECAL, ENSEMBLVEP_DOWNLOAD, GATK4_GATHERBQSRREPORTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT, TABIX_BGZIPTABIX, GATK4_MARKDUPLICATES_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES, GATK4_CREATESEQUENCEDICTIONARY, CALCULATECONTAMINATION, MERGE_DEEPVARIANT_GVCF, COLLATE_FASTQ_MAP, TABIX_VC_FREEBAYES, MOSDEPTH, MERGE_STRELKA_INDELS, UNZIP, COLLATE_FASTQ_UNMAP, UNZIP_GC, VCFTOOLS_TSTV_COUNT, GATK4_MERGEMUTECTSTATS, CAT_MPILEUP, CONTROLFREEC_ASSESSSIGNIFICANCE, MANTA_TUMORONLY, BWAMEM2_INDEX, MERGE_STRELKA_SNVS, SAMTOOLS_VIEW_MAP_UNMAP, NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI, MERGE_STRELKA, BCFTOOLS_CONCAT, SAMTOOLS_INDEX, MERGE_CRAM, GATK4_CNNSCOREVARIANTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP, TABIX_BGZIP_TIDDIT_SV, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED, TABIX_PON, VARIANTRECALIBRATOR_SNP, TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS, UNTAR_CHR_DIR, FREEC_TUMORONLY, SAMBLASTER, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH, FREEBAYES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP, GATHERPILEUPSUMMARIES, NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL, INDEX_CRAM, SAMTOOLS_MPILEUP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ, BCFTOOLS_SORT, MANTA_SOMATIC, NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS, GATK4_FILTERMUTECTCALLS, MERGE_VQSR, MUTECT2_PAIRED, BWAMEM1_INDEX, GATK4_GATHERPILEUPSUMMARIES, DRAGMAP_HASHTABLE, CNVKIT_ANTITARGET, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN, GATK4_MARKDUPLICATES, SAMTOOLS_VIEW_UNMAP_MAP, SAMTOOLS_CONVERT, TABIX_GERMLINE_VCFS_CONCAT_SORT, TABIX_VC_DEEPVARIANT_VCF, MERGE_STRELKA_GENOME, CONTROLFREEC_FREEC2BED, TABIX_VC_DEEPVARIANT_GVCF, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP, BAM2FASTQ, UNZIP_RT, SAMTOOLS_COLLATEFASTQ, MERGEMUTECTSTATS, GATK4_APPLYVQSR, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM, GATK4_CALCULATECONTAMINATION, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS, DEEPVARIANT, GATK4_GENOTYPEGVCFS, MSISENSORPRO_MSI_SOMATIC, FREEC2CIRCOS, DRAGMAP_ALIGN, GATK4_INTERVALLISTTOBED, GATK4_APPLYVQSR_INDEL, FGBIO_GROUPREADSBYUMI, BCFTOOLS_MPILEUP, SAMTOOLS_VIEW, CNVKIT_BATCH, FGBIO_CALLMOLECULARCONSENSUSREADS, GETPILEUPSUMMARIES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP, GETPILEUPSUMMARIES_NORMAL, GATK4_GENOMICSDBIMPORT, MERGE_MUTECT2, GATK4_BASERECALIBRATOR_SPARK, ASCAT Aug-07 09:45:45.100 [main] WARN nextflow.Session - There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS? Aug-07 09:45:45.103 [main] DEBUG nextflow.Session - Igniting dataflow network (120) Aug-07 09:45:45.111 [PathVisitor-2] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz; options: [:] Aug-07 09:45:45.120 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC Aug-07 09:45:45.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT Aug-07 09:45:45.130 [PathVisitor-8] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /TEST/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi; options: [:] Aug-07 09:45:45.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Aug-07 09:45:45.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Aug-07 09:45:45.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Aug-07 09:45:45.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Aug-07 09:45:45.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Aug-07 09:45:45.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Aug-07 09:45:45.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Aug-07 09:45:45.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Aug-07 09:45:45.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Aug-07 09:45:45.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Aug-07 09:45:45.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Aug-07 09:45:45.133 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC Aug-07 09:45:45.133 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP Aug-07 09:45:45.133 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM Aug-07 09:45:45.134 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR Aug-07 09:45:45.135 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS Aug-07 09:45:45.135 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR Aug-07 09:45:45.135 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM Aug-07 09:45:45.135 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM Aug-07 09:45:45.135 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS Aug-07 09:45:45.141 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH Aug-07 09:45:45.142 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL Aug-07 09:45:45.142 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Aug-07 09:45:45.153 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC Aug-07 09:45:45.153 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Aug-07 09:45:45.153 [main] DEBUG nextflow.Session - Session await Aug-07 09:45:45.271 [Actor Thread 30] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.014 s; total time: 0.015 s Aug-07 09:45:45.271 [Actor Thread 37] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.014 s; total time: 0.015 s Aug-07 09:45:45.297 [Actor Thread 30] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /TEST/work/collect-file/90ab199327720f1891d40a7e49030566 Aug-07 09:45:45.299 [Actor Thread 37] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /TEST/work/collect-file/6f2c54c250c688594beef61ca8ef28da Aug-07 09:45:45.305 [Actor Thread 30] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-11592197438853572220 Aug-07 09:45:45.305 [Actor Thread 37] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7076156243468410628 Aug-07 09:45:45.423 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38) > jobId: 2527; workDir: /TEST/work/5d/d48638c297d7faee23162455783b61 Aug-07 09:45:45.423 [Task submitter] INFO nextflow.Session - [5d/d48638] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38) Aug-07 09:45:45.468 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1) > jobId: 2528; workDir: /TEST/work/92/9e05db326304821b3e2f2e4b2d93af Aug-07 09:45:45.468 [Task submitter] INFO nextflow.Session - [92/9e05db] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1) Aug-07 09:45:45.506 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1) > jobId: 2529; workDir: /TEST/work/91/26c61fe6c3f750cd8cd889cacbbaa5 Aug-07 09:45:45.506 [Task submitter] INFO nextflow.Session - [91/26c61f] Submitted process > NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1) Aug-07 09:45:45.549 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed) > jobId: 2530; workDir: /TEST/work/08/98ec0cdc54fa2b789584af47f79b98 Aug-07 09:45:45.549 [Task submitter] INFO nextflow.Session - [08/98ec0c] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed) Aug-07 09:45:49.346 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 2527; id: 10; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38); status: COMPLETED; exit: 126; error: -; workDir: /TEST/work/5d/d48638c297d7faee23162455783b61 started: 1691401549342; exited: 2023-08-07T09:45:46.536Z; ] Aug-07 09:45:49.349 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38); work-dir=/TEST/work/5d/d48638c297d7faee23162455783b61 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)` terminated with an error exit status (126) Aug-07 09:45:49.371 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)' Caused by: Process `NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)` terminated with an error exit status (126) Command executed: bgzip --threads 1 -c wgs_calling_regions_noseconds.hg38.bed > wgs_calling_regions_noseconds.hg38.bed.gz tabix wgs_calling_regions_noseconds.hg38.bed.gz cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED": tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//') END_VERSIONS Command exit status: 126 Command output: (empty) Command error: docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-K5tl3VTLATq7DuPAOQjeQBu6": dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'. Work dir: /TEST/work/5d/d48638c297d7faee23162455783b61 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` Aug-07 09:45:49.380 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Aug-07 09:45:49.397 [main] DEBUG nextflow.Session - Session await > all processes finished Aug-07 09:45:49.398 [Actor Thread 29] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Aug-07 09:45:49.398 [Actor Thread 43] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Aug-07 09:45:49.399 [Actor Thread 25] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Aug-07 09:45:49.399 [Actor Thread 42] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Aug-07 09:45:49.400 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:MULTIQC; work-dir=null error [java.lang.IllegalStateException]: Cannot obtain the semaphore to fork operator's body. Aug-07 09:45:49.401 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 2528; id: 16; name: NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1); status: COMPLETED; exit: 126; error: -; workDir: /TEST/work/92/9e05db326304821b3e2f2e4b2d93af started: 1691401549399; exited: 2023-08-07T09:45:46.527Z; ] Aug-07 09:45:49.401 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1); work-dir=/TEST/work/92/9e05db326304821b3e2f2e4b2d93af error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)` terminated with an error exit status (126) Aug-07 09:50:49.346 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[jobId: 2529; id: 17; name: NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1); status: SUBMITTED; exit: -; error: -; workDir: /TEST/work/91/26c61fe6c3f750cd8cd889cacbbaa5 started: -; exited: -; ] ~> TaskHandler[jobId: 2530; id: 18; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed); status: SUBMITTED; exit: -; error: -; workDir: /TEST/work/08/98ec0cdc54fa2b789584af47f79b98 started: -; exited: -; ] Aug-07 09:55:19.359 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 2529; id: 17; name: NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1); status: COMPLETED; exit: 0; error: -; workDir: /TEST/work/91/26c61fe6c3f750cd8cd889cacbbaa5 started: 1691402104360; exited: 2023-08-07T09:54:37.194Z; ] Aug-07 09:55:19.508 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Aug-07 09:55:19.508 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Aug-07 09:55:19.523 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Aug-07 09:55:19.535 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 2530; id: 18; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed); status: COMPLETED; exit: 0; error: -; workDir: /TEST/work/08/98ec0cdc54fa2b789584af47f79b98 started: 1691402104362; exited: 2023-08-07T09:54:37.339Z; ] Aug-07 09:55:19.547 [main] DEBUG nextflow.Session - Session await > all barriers passed Aug-07 09:55:19.581 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Aug-07 09:55:19.585 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/sarek][0;31m Pipeline completed with errors[0m- Aug-07 09:55:19.589 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=2; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=9s; failedDuration=11ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=9; peakMemory=5 GB; ] Aug-07 09:55:19.589 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Aug-07 09:55:19.594 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Aug-07 09:55:19.612 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":null,"process":"TABIX_BGZIPTABIX_INTERVAL_COMBINED","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":3,"min":3,"q1":3,"q2":3,"q3":3,"max":3,"minLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)","maxLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)","q1Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)","q2Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)","q3Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)"},"writes":null},{"cpuUsage":null,"process":"FASTQC","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":2,"min":2,"q1":2,"q2":2,"q3":2,"max":2,"minLabel":"NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)","maxLabel":"NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)","q1Label":"NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)","q2Label":"NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)","q3Label":"NFCORE_SAREK:SAREK:FASTQC (test_sample-lane_1)"},"writes":null},{"cpuUsage":{"mean":9.91,"min":9.91,"q1":9.91,"q2":9.91,"q3":9.91,"max":9.91,"minLabel":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","maxLabel":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","q1Label":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","q2Label":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","q3Label":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)"},"process":"FASTP","mem":{"mean":3293184,"min":3293184,"q1":3293184,"q2":3293184,"q3":3293184,"max":3293184,"minLabel":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","maxLabel":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","q1Label":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","q2Label":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","q3Label":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)"},"memUsage":{"mean":0.08,"min":0.08,"q1":0.08,"q2":0.08,"q3":0.08,"max":0.08,"minLabel":"NFCORE_SAREK:SAREK:FASTP (test_sample-lane_1)","maxLabel":"NFCORE_SAREK:SAREK:FASTP 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(wgs_calling_regions_noseconds.hg38.bed)","q3Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed)"}}] Aug-07 09:55:20.235 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Aug-07 09:55:20.553 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Aug-07 09:55:20.642 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Aug-07 09:55:20.644 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-K5tl3VTLATq7DuPAOQjeQBu6": dial unix /var/run/docker.sock: connect: permission denied.

nf-core / sarek

sarek in slurm : issue #1165

!/bin/bash

SBATCH --qos=standard

SBATCH --job-name=cd_301

SBATCH --nodes=1

SBATCH --tasks=2

SBATCH --cpus-per-task=8

SBATCH --tasks-per-node=1

SBATCH --output=/TEST/sarek301%j.out

SBATCH --chdir=/TEST/

SBATCH --error=/TEST/sarek300%j.err

It is giving me this