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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Unexpected error [UnsupportedOperationException] when running the test case #799

Closed shaojunyu closed 2 years ago

shaojunyu commented 2 years ago

Description of the bug

Unexpected error [UnsupportedOperationException] when running the test case

Command used and terminal output

$ nextflow run nf-core/sarek -profile test_full,docker --outdir out

Relevant files

Oct-14 12:07:56.647 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -profile test_full,docker --outdir out Oct-14 12:07:56.699 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.10.6 Oct-14 12:07:57.456 [main] DEBUG nextflow.scm.AssetManager - Git config: /users/syu86/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git Oct-14 12:07:57.466 [main] DEBUG nextflow.scm.AssetManager - Git config: /users/syu86/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git Oct-14 12:07:57.529 [main] INFO nextflow.cli.CmdRun - Launching nf-core/sarek [festering_volta] - revision: bcd7bf9cb9 [master] Oct-14 12:07:57.873 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /users/syu86/.nextflow/assets/nf-core/sarek/nextflow.config Oct-14 12:07:57.873 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mydata/nf_gwas/nextflow.config Oct-14 12:07:57.873 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /users/syu86/.nextflow/assets/nf-core/sarek/nextflow.config Oct-14 12:07:57.873 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mydata/nf_gwas/nextflow.config Oct-14 12:07:57.880 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: test_full,docker Oct-14 12:07:58.133 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Oct-14 12:07:58.141 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-14 12:07:58.142 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-14 12:07:58.144 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Oct-14 12:07:58.147 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Oct-14 12:07:58.307 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Oct-14 12:07:58.307 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Oct-14 12:07:59.148 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: test_full,docker Oct-14 12:07:59.163 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, tigem, google, use_gatk_spark, eddie, medair, alignment_to_fastq, bi, bigpurple, sbc_sharc, adcra, cedars, tools, utd_ganymede, charliecloud, targeted, icr_davros, save_bam_mapped, munin, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, awsbatch, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, cheaha, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, gis, umi, eva, markduplicates_bam, fgcz, conda, singularity, prince, hebbe, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, uct_hpc, aws_tower, binac] Oct-14 12:07:59.196 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/users/syu86/.nextflow/plugins Oct-14 12:07:59.197 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Oct-14 12:07:59.200 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-14 12:07:59.200 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-14 12:07:59.201 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Oct-14 12:07:59.208 [main] INFO org.pf4j.AbstractPluginManager - No plugins Oct-14 12:07:59.248 [main] DEBUG nextflow.Session - Session uuid: b179f581-bd07-4059-b472-25858bdfa43e Oct-14 12:07:59.248 [main] DEBUG nextflow.Session - Run name: festering_volta Oct-14 12:07:59.249 [main] DEBUG nextflow.Session - Executor pool size: 144 Oct-14 12:07:59.274 [main] DEBUG nextflow.cli.CmdRun - Version: 21.10.6 build 5660 Created: 21-12-2021 16:55 UTC (09:55 MDT) System: Linux 5.4.0-100-generic Runtime: Groovy 3.0.9 on OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21 Encoding: UTF-8 (UTF-8) Process: 125630@node0.syu86-135964.latencymodel-pg0.clemson.cloudlab.us [130.127.134.38] CPUs: 144 - Mem: 251.2 GB (209.9 GB) - Swap: 3 GB (3 GB) Oct-14 12:07:59.284 [main] DEBUG nextflow.Session - Work-dir: /mydata/nf_gwas/work [ext2/ext3] Oct-14 12:07:59.284 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /users/syu86/.nextflow/assets/nf-core/sarek/bin Oct-14 12:07:59.291 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Oct-14 12:07:59.299 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-14 12:07:59.398 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 145; maxThreads: 1000 Oct-14 12:07:59.456 [main] DEBUG nextflow.Session - Session start invoked Oct-14 12:07:59.461 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /mydata/nf_gwas/out/pipeline_info/execution_trace_2022-10-14_12-07-58.txt Oct-14 12:07:59.469 [main] DEBUG nextflow.Session - Using default localLib path: /users/syu86/.nextflow/assets/nf-core/sarek/lib Oct-14 12:07:59.472 [main] DEBUG nextflow.Session - Adding to the classpath library: /users/syu86/.nextflow/assets/nf-core/sarek/lib Oct-14 12:07:59.473 [main] DEBUG nextflow.Session - Adding to the classpath library: /users/syu86/.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar Oct-14 12:08:00.178 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-14 12:08:00.376 [main] INFO nextflow.Nextflow -

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 nf-core/sarek v3.0.2 ------------------------------------------------------ Core Nextflow options revision : master runName : festering_volta containerEngine : docker launchDir : /mydata/nf_gwas workDir : /mydata/nf_gwas/work projectDir : /users/syu86/.nextflow/assets/nf-core/sarek userName : syu86 profile : test_full,docker configFiles : /users/syu86/.nextflow/assets/nf-core/sarek/nextflow.config, /mydata/nf_gwas/nextflow.config

Input/output options input : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv outdir : out

Main options split_fastq : 20000000 wes : true intervals : s3://nf-core-awsmegatests/sarek/input/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed tools : strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep

Variant Calling pon : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz pon_tbi : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi

Reference genome options ascat_genome : hg38 ascat_alleles : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip ascat_loci : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip ascat_loci_gc : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip ascat_loci_rt : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip bwa : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/ bwamem2 : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/ chr_dir : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes dbsnp : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz dbsnp_tbi : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi dbsnp_vqsr : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz dict : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict dragmap : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/ fasta : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta fasta_fai : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai germline_resource : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz germline_resource_tbi : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi known_indels : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz known_indels_tbi : s3://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 known_indels_vqsr : --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 known_snps : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz known_snps_tbi : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi known_snps_vqsr : --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz mappability : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem snpeff_db : GRCh38.105 snpeff_genome : GRCh38 snpeff_version : 5.1 vep_genome : GRCh38 vep_species : homo_sapiens vep_cache_version : 106 vep_version : 106.1 igenomes_base : s3://ngi-igenomes/igenomes

Institutional config options config_profile_name : Full test profile config_profile_description: Full test dataset to check pipeline function

!! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/sarek for your analysis please cite:

System information

shaojunyu commented 2 years ago

updating to Java 18 solved this problem