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problems running v1.6.1 #65

Closed carolinehey closed 1 year ago

carolinehey commented 1 year ago

Operating System

Windows 10

Other Linux

No response

Workflow Version

v1.6.1

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-human-variation -w /data/wf_hum_C -profile standard --methyl --bam /longread/G119-2021/Kit14/23RKG000340/23RKG00340_03072023_dorado_5hm_5mc_hac.bam --ref /longread/resources/reference_genomes/T2T/T2T-CHM13v2.0/logic_names/ALL_CAPS/T2T-CHM13v2_reference.fasta --sample_name 23RK000340_test --out_dir /longread/G119-2021/Kit14/23RKG000340/human-variation-test

Workflow Execution - CLI Execution Profile

None

What happened?

Recently i have had some problems running the workflow. I had no problems running v1.5.2 of the workflow on this file, but other ubam files fails both v1.6.1 and v1.5.2. This i the error log output from v.1.6.1.

Relevant log output

Aug-03 08:34:32.820 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-human-variation -w /data/wf_hum_C -profile standard --methyl --bam /longread/G119-2021/Kit14/23RKG000340/23RKG00340_03072023_dorado_5hm_5mc_hac.bam --ref /longread/resources/reference_genomes/T2T/T2T-CHM13v2.0/logic_names/ALL_CAPS/T2T-CHM13v2_reference.fasta --sample_name 23RK000340_test --out_dir /longread/G119-2021/Kit14/23RKG000340/human-variation-test
Aug-03 08:34:34.011 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2
Aug-03 08:34:34.039 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.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-03 08:34:34.326 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-03 08:34:34.328 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-03 08:34:34.332 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-03 08:34:34.347 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Aug-03 08:34:34.366 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /root/.nextflow/scm
Aug-03 08:34:35.389 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/epi2me-labs/wf-human-variation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-human-variation.git
Aug-03 08:34:35.406 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Aug-03 08:34:35.429 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/epi2me-labs/wf-human-variation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-human-variation.git
Aug-03 08:34:36.291 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /root/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config
Aug-03 08:34:36.295 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config
Aug-03 08:34:36.304 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Aug-03 08:34:36.467 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Aug-03 08:34:36.467 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/epi2me-labs/wf-human-variation [friendly_plateau] DSL2 - revision: e2f6b6a [master]
Aug-03 08:34:36.468 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-03 08:34:36.468 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Aug-03 08:34:36.470 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Aug-03 08:34:36.472 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@149c39b] - activable => nextflow.secret.LocalSecretsProvider@149c39b
Aug-03 08:34:36.520 [main] DEBUG nextflow.Session - Session UUID: 18d95e8f-6a4f-40f8-b9a9-419dd8eeccf8
Aug-03 08:34:36.520 [main] DEBUG nextflow.Session - Run name: friendly_plateau
Aug-03 08:34:36.520 [main] DEBUG nextflow.Session - Executor pool size: 64
Aug-03 08:34:36.529 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-03 08:34:36.551 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.04.2 build 5870
Created: 08-06-2023 08:29 UTC (10:29 CEST)
System: Linux 4.15.0-197-generic
Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.17+8-post-Ubuntu-1ubuntu218.04
Encoding: UTF-8 (UTF-8)
Process: 63712@srvodeappgsq02 [10.161.6.233]
CPUs: 64 - Mem: 376.5 GB (68 GB) - Swap: 8 GB (8 GB)
Aug-03 08:34:36.634 [main] DEBUG nextflow.Session - Work-dir: /data/wf_hum_C [ext2/ext3]
Aug-03 08:34:36.648 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-03 08:34:36.657 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-03 08:34:36.730 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-03 08:34:36.739 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000
Aug-03 08:34:38.628 [main] DEBUG nextflow.Session - Session start
Aug-03 08:34:38.639 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /longread/G119-2021/Kit14/23RKG000340/human-variation-test/execution/trace.txt
Aug-03 08:34:38.757 [main] DEBUG nextflow.Session - Using default localLib path: /root/.nextflow/assets/epi2me-labs/wf-human-variation/lib
Aug-03 08:34:38.762 [main] DEBUG nextflow.Session - Adding to the classpath library: /root/.nextflow/assets/epi2me-labs/wf-human-variation/lib
Aug-03 08:34:38.763 [main] DEBUG nextflow.Session - Adding to the classpath library: /root/.nextflow/assets/epi2me-labs/wf-human-variation/lib/nfcore_external_java_deps.jar
Aug-03 08:34:40.470 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-03 08:34:44.344 [main] INFO nextflow.Nextflow -
�[0;92m|||||||||| �[0m�[2m_____ ____ ___ ____ __ __ _____ _ _
�[0;92m|||||||||| �[0m�[2m| | _ _ | | / | | | | __ | | ___
�[0;33m||||| �[0m�[2m| | | |) | | __) | |/| | | _| |/ ` | ' / |
�[0;33m||||| �[0m�[2m| || /| | / /| | | | ||| | (| | |) _
�[0;94m|||||||||| �[0m�[2m|_____|| |||| ||| ||_,|./|__/
�[0;94m|||||||||| �[0m�[1mwf-human-variation v1.6.1-ge2f6b6a�[0m
�[2m--------------------------------------------------------------------------------�[0m
�[1mCore Nextflow options�[0m
�[0;34mrevision : �[0;32mmaster�[0m
�[0;34mrunName : �[0;32mfriendly_plateau�[0m
�[0;34mcontainerEngine : �[0;32mdocker�[0m
�[0;34mcontainer : �[0;32montresearch/wf-human-variation:sha95dd6fedf10c10fc65bdff3c2c48a1af2adcc8c0�[0m
�[0;34mlaunchDir : �[0;32m/longread/G119-2021/Kit14/23RKG000340�[0m
�[0;34mworkDir : �[0;32m/data/wf_hum_C�[0m
�[0;34mprojectDir : �[0;32m/root/.nextflow/assets/epi2me-labs/wf-human-variation�[0m
�[0;34muserName : �[0;32mroot�[0m
�[0;34mprofile : �[0;32mstandard�[0m
�[0;34mconfigFiles : �[0;32m/root/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config�[0m

�[1mWorkflow Options�[0m
�[0;34mmethyl : �[0;32mtrue�[0m

�[1mInput Options�[0m
�[0;34mbam : �[0;32m/longread/G119-2021/Kit14/23RKG000340/23RKG00340_03072023_dorado_5hm_5mc_hac.bam�[0m
�[0;34mref : �[0;32m/longread/resources/reference_genomes/T2T/T2T-CHM13v2.0/logic_names/ALL_CAPS/T2T-CHM13v2_reference.fasta�[0m

�[1mOutput Options�[0m
�[0;34msample_name : �[0;32m23RK000340_test�[0m
�[0;34mout_dir : �[0;32m/longread/G119-2021/Kit14/23RKG000340/human-variation-test�[0m

�[1mMultiprocessing Options�[0m
�[0;34mubam_map_threads : �[0;32m8�[0m
�[0;34mubam_sort_threads : �[0;32m3�[0m
�[0;34mubam_bam2fq_threads: �[0;32m1�[0m

�[1mOther parameters�[0m
�[0;34mprocess_label : �[0;32mwfdefault�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
�[2m--------------------------------------------------------------------------------�[0m
If you use epi2me-labs/wf-human-variation for your analysis please cite:

The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
�[2m--------------------------------------------------------------------------------�[0m
This is epi2me-labs/wf-human-variation v1.6.1-ge2f6b6a.
�[2m--------------------------------------------------------------------------------�[0m
Aug-03 08:34:45.028 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.028 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.034 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Aug-03 08:34:45.039 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=12 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
Aug-03 08:34:45.125 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.125 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.144 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.165 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.165 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.175 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.175 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.187 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.187 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.204 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_human_snp matches labels wf_human_snp for process with name readStats
Aug-03 08:34:45.204 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.204 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.210 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.210 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.212 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.212 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.214 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.214 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.236 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.236 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.258 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.258 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.266 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_human_methyl matches labels wf_human_methyl for process with name methyl:modbam2bed
Aug-03 08:34:45.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.270 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.271 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.287 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-03 08:34:45.287 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-03 08:34:45.291 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: filterBam, get_qual_filter, intersectBedWithTruthset, annotate_snp_vcf, makeAlignmentReport, merge_calls_to_fastq, qsFilter, create_candidates, sortVCF, index_ref_gzi, indexVCF, filterBenchmarkVcf, makeReport, hap, select_het_snps, make_mmi, getVersions, bam_ingress:cram_to_bam, callCNV, output_snp, annotate_vcf, pileup_variants, methyl:modbam2bed, bam_ingress:samtools_index, merge_vcf, phase_contig, aggregate_full_align_variants, merge_tsv, cram_to_bam, bam_ingress:check_for_alignment, merge_haplotagged_contigs, getAllChromosomesBed, phase_contig_haplotag, post_clair_phase_contig, output_cnv, configure_jbrowse, check_for_alignment, samtools_index, getParams, merge_pileup_and_full_vars, make_report, refine_with_sv, mapula, annotate_repeat_expansions, sniffles2, output_sv, readStats, evaluate_candidates, get_coverage, aggregate_pileup_variants, lookup_clair3_model, index_ref_fai, truvari, filterCalls, minimap2_alignment, merge_fail_calls, publish_artifact, failedQCReport, make_chunks, output_str, bam_ingress:minimap2_alignment, cram_cache, merge_pass_calls_to_fastq, call_str, vcfStats, getGenome, merge_calls, merge_pass_calls, mosdepth, dorado, merge_fail_calls_to_fastq, decompress_ref, aggregate_all_variants, report, modbam2bed, align_and_qsFilter
Aug-03 08:34:45.293 [main] DEBUG nextflow.Session - Igniting dataflow network (25)
Aug-03 08:34:45.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > bam_ingress:samtools_index
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > bam_ingress:check_for_alignment
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > bam_ingress:cram_to_bam
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > bam_ingress:minimap2_alignment
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > cram_cache
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > getAllChromosomesBed
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > mosdepth
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > readStats
Aug-03 08:34:45.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > getVersions
Aug-03 08:34:45.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > getParams
Aug-03 08:34:45.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > get_coverage
Aug-03 08:34:45.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > failedQCReport
Aug-03 08:34:45.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > makeAlignmentReport
Aug-03 08:34:45.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > methyl:modbam2bed
Aug-03 08:34:45.302 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > configure_jbrowse
Aug-03 08:34:45.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > publish_artifact
Aug-03 08:34:45.306 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Aug-03 08:34:45.306 [main] DEBUG nextflow.Session - Session await
Aug-03 08:34:45.505 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:34:45.508 [Task submitter] INFO nextflow.Session - [41/9367f5] Submitted process > cram_cache (1)
Aug-03 08:34:45.513 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:34:45.513 [Task submitter] INFO nextflow.Session - [b1/7719cb] Submitted process > getVersions
Aug-03 08:34:45.517 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:34:45.518 [Task submitter] INFO nextflow.Session - [15/5c1c78] Submitted process > getParams
Aug-03 08:34:45.522 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:34:45.523 [Task submitter] INFO nextflow.Session - [66/5001bd] Submitted process > publish_artifact (1)
Aug-03 08:34:45.526 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:34:45.526 [Task submitter] INFO nextflow.Session - [28/e86409] Submitted process > bam_ingress:samtools_index (1)
Aug-03 08:34:47.296 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: getVersions; status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/b1/7719cbd749b415c4fbc94399e48118]
Aug-03 08:34:47.430 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: getParams; status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/15/5c1c781853925b387d18065425bb6e]
Aug-03 08:34:47.514 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: publish_artifact (1); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/66/5001bd5f0f46c6dd77f99d53387dc9]
Aug-03 08:34:47.553 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-03 08:36:11.839 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: cram_cache (1); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/41/9367f596efa2578983b90d361e54ab]
Aug-03 08:36:11.864 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:36:11.864 [Task submitter] INFO nextflow.Session - [87/4acb72] Submitted process > publish_artifact (4)
Aug-03 08:36:12.147 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:36:12.148 [Task submitter] INFO nextflow.Session - [a7/040c2a] Submitted process > publish_artifact (3)
Aug-03 08:36:12.320 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:36:12.320 [Task submitter] INFO nextflow.Session - [b3/c0ad39] Submitted process > getAllChromosomesBed (1)
Aug-03 08:36:12.327 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 08:36:12.333 [Task submitter] INFO nextflow.Session - [f0/59b534] Submitted process > publish_artifact (2)
Aug-03 08:36:13.199 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: publish_artifact (4); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/87/4acb721820ff5325fd60e9aecbe7c7]
Aug-03 08:36:16.090 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: publish_artifact (3); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/a7/040c2a9d6493d40a3f0c3728d89548]
Aug-03 08:36:16.471 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: publish_artifact (2); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/f0/59b534b290ac24fca8f1187649b04a]
Aug-03 08:37:41.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: getAllChromosomesBed (1); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/b3/c0ad398e28ba56cad98dae081ddf10]
Aug-03 08:39:45.240 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: bam_ingress:samtools_index (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/28/e8640917b42aa76331c6b17e83b3dc]
Aug-03 08:44:45.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: bam_ingress:samtools_index (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/28/e8640917b42aa76331c6b17e83b3dc]
Aug-03 08:49:45.323 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: bam_ingress:samtools_index (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/28/e8640917b42aa76331c6b17e83b3dc]
Aug-03 08:54:45.336 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: bam_ingress:samtools_index (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/28/e8640917b42aa76331c6b17e83b3dc]
Aug-03 08:59:45.354 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: bam_ingress:samtools_index (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/28/e8640917b42aa76331c6b17e83b3dc]
Aug-03 09:00:33.194 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: bam_ingress:samtools_index (1); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/28/e8640917b42aa76331c6b17e83b3dc]
Aug-03 09:00:40.901 [Actor Thread 54] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/epi2me-labs/wf-human-variation/bin/workflow-glue
Aug-03 09:00:40.918 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 09:00:40.919 [Task submitter] INFO nextflow.Session - [76/e4cb98] Submitted process > bam_ingress:check_for_alignment (1)
Aug-03 09:01:01.515 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: bam_ingress:check_for_alignment (1); status: COMPLETED; exit: 0; error: -; workDir: /data/wf_hum_C/76/e4cb98382a653d2c6d46a4d7ab5b36]
Aug-03 09:01:01.622 [Actor Thread 40] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/epi2me-labs/wf-human-variation/data/OPTIONAL_FILE
Aug-03 09:01:01.637 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-03 09:01:01.638 [Task submitter] INFO nextflow.Session - [b1/ae61fb] Submitted process > bam_ingress:minimap2_alignment (1)
Aug-03 09:04:45.370 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 11; name: bam_ingress:minimap2_alignment (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/b1/ae61fbe123d435fb1152a95be128e9]
...
Aug-03 14:54:48.291 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 11; name: bam_ingress:minimap2_alignment (1); status: RUNNING; exit: -; error: -; workDir: /data/wf_hum_C/b1/ae61fbe123d435fb1152a95be128e9]
Aug-03 14:58:15.337 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: bam_ingress:minimap2_alignment (1); status: COMPLETED; exit: 1; error: -; workDir: /data/wf_hum_C/b1/ae61fbe123d435fb1152a95be128e9]
Aug-03 14:58:15.347 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=bam_ingress:minimap2_alignment (1); work-dir=/data/wf_hum_C/b1/ae61fbe123d435fb1152a95be128e9
error [nextflow.exception.ProcessFailedException]: Process bam_ingress:minimap2_alignment (1) terminated with an error exit status (1)
Aug-03 14:58:15.362 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'bam_ingress:minimap2_alignment (1)'

Caused by:
Process bam_ingress:minimap2_alignment (1) terminated with an error exit status (1)

Command executed:

samtools bam2fq -@ 1 -T 1 23RKG00340_03072023_dorado_5hm_5mc_hac.bam | minimap2 -y -t 8 -ax map-ont T2T-CHM13v2_reference.fasta - | samtools sort -@ 3 --write-index -o 23RK000340_test.cram##idx##23RK000340_test.cram.crai -O cram --reference T2T-CHM13v2_reference.fasta -

Command exit status:
1

Command output:
(empty)

Command error:
[M::worker_pipeline::11136.1987.13] mapped 134300 sequences
...
[M::worker_pipeline::21229.7956.79] mapped 150189 sequences
[E::sam_parse1] SEQ and QUAL are of different length
samtools sort: truncated file. Aborting

Work dir:
/data/wf_hum_C/b1/ae61fbe123d435fb1152a95be128e9

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
Aug-03 14:58:15.367 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process bam_ingress:minimap2_alignment (1) terminated with an error exit status (1)
Aug-03 14:58:15.375 [main] DEBUG nextflow.Session - Session await > all processes finished
Aug-03 14:58:15.899 [main] DEBUG nextflow.Session - Session await > all barriers passed
Aug-03 14:58:15.965 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=10; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=28m 49s; failedDuration=2d 23h 26m 43s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=5; peakCpus=12; peakMemory=12 GB; ]
Aug-03 14:58:15.965 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Aug-03 14:58:15.969 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Aug-03 14:58:16.022 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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Aug-03 14:58:17.083 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Aug-03 14:58:17.600 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Aug-03 14:58:17.885 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Application activity log entry

No response

cjw85 commented 1 year ago

Hi @carolinehey,

The error:

[M::worker_pipeline::21229.7956.79] mapped 150189 sequences
[E::sam_parse1] SEQ and QUAL are of different length
samtools sort: truncated file. Aborting

suggests that the input BAM file is malformed. Can you report the version of dorado used for basecalling. This is not the first time we have seen this error and is an error with the basecaller not the workflow.

carolinehey commented 1 year ago

Yes, but the exact same file works with no errors using v.1.5.2. image

The dorado version is 0.3.0

cjw85 commented 1 year ago

Can you run the following on your input file:

samtools quickcheck

The other possibility here is that one of the proceses (likely minimap2) used a large amount of memory and died; the error we see being a side effect rather than the ultimately cause.

I will pass you on to @SamStudio8 to aid you further.

carolinehey commented 1 year ago

Thank you @cjw85 . samtools quickcheck 23RKG00340_03072023_dorado_5hm_5mc_hac.bam 23RKG00340_03072023_dorado_5hm_5mc_hac.bam had no targets in header.

the file is uBAM.

SamStudio8 commented 1 year ago

Yes, Chris' observation seems likely. We should try and increase the memory allocated to the minimap process. You can do this by using Nextflow process selectors to apply configuration to particular parts of our workflow. To increase the memory for a process called “minimap2_alignment”, create a file (for example, named increase_memory.config) with the following configuration:


process {
    withName:minimap2_alignment {
        memory = "24 GB"
    }
}

When invoking Nextflow with nextflow run, reference this extra configuration with -c increase_memory.config. If you continue to observe this error you may need to fine tune the memory value.