Comet "segfault-like" error when running test pipeline under WSL2

radusuciu commented 1 year ago

Description of the bug

I hit this error after installing the latest version of nextflow and running the test_lfq,docker profile: Standard error: Process '/usr/local/bin/comet.exe' crashed hard (segfault-like). Please check the log. The log is not really all that more informative unfortunately.

I suspect this error may be related to running under WSL2, as @lazear has experienced something similar with the mhcquant pipeline. I haven't had time to test in a different environment, but was wondering if others have experienced similar issues and if there are any workarounds.

Command used and terminal output

Log

```console May-10 10:51:50.945 [main] DEBUG nextflow.cli.Launcher - $> nextflow run bigbio/quantms -r dev -profile test_lfq,docker May-10 10:51:51.154 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 May-10 10:51:51.183 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/radu/.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@0.8.2 May-10 10:51:51.206 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-10 10:51:51.211 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-10 10:51:51.218 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-10 10:51:51.255 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-10 10:51:51.275 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/radu/.nextflow/scm May-10 10:51:52.852 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/radu/.nextflow/assets/bigbio/quantms/.git/config; branch: master; remote: origin; url: https://github.com/bigbio/quantms.git May-10 10:51:52.879 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] May-10 10:51:52.890 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/radu/.nextflow/assets/bigbio/quantms/.git/config; branch: master; remote: origin; url: https://github.com/bigbio/quantms.git May-10 10:51:53.950 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/radu/.nextflow/assets/bigbio/quantms/nextflow.config May-10 10:51:53.953 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/radu/.nextflow/assets/bigbio/quantms/nextflow.config May-10 10:51:53.967 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test_lfq,docker` May-10 10:51:55.555 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, mambaci, denbi_qbic, alice, mjolnir_globe, uppmax, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, eddie, test_localize, medair, test_full_tmt, test_tmt, bi, bigpurple, sbc_sharc, adcra, cedars, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, genotoul, abims, ebicluster, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, cambridge, micromamba, podman, test_lfq, cheaha, xanadu, test, computerome, test_full_lfq, seg_globe, sanger, dkfz, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, psmn, eva, fgcz, conda, crg, singularity, prince, utd_sysbio, test_full_dia, debug, test_dia, genouest, cbe, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac] May-10 10:51:55.678 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion May-10 10:51:55.681 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/bigbio/quantms` [infallible_leibniz] DSL2 - revision: 7363d90536 [dev] May-10 10:51:55.683 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-10 10:51:55.684 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] May-10 10:51:55.723 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/radu/.nextflow/secrets/store.json May-10 10:51:55.742 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3ace6346] - activable => nextflow.secret.LocalSecretsProvider@3ace6346 May-10 10:51:55.879 [main] DEBUG nextflow.Session - Session UUID: e77c1508-f04f-45b1-a287-c4c468b50899 May-10 10:51:55.880 [main] DEBUG nextflow.Session - Run name: infallible_leibniz May-10 10:51:55.882 [main] DEBUG nextflow.Session - Executor pool size: 20 May-10 10:51:55.912 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-10 10:51:55.961 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.1 build 5866 Created: 15-04-2023 06:51 UTC (14-04-2023 23:51 PDT) System: Linux 5.15.90.1-microsoft-standard-WSL2 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.18+10-post-Ubuntu-0ubuntu122.04 Encoding: UTF-8 (UTF-8) Process: 1580668@US320024WSD [127.0.1.1] CPUs: 20 - Mem: 31.2 GB (5.3 GB) - Swap: 8 GB (5.9 GB) May-10 10:51:56.025 [main] DEBUG nextflow.Session - Work-dir: /mnt/d/processing/quantms/work [v9fs] May-10 10:51:56.052 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-10 10:51:56.079 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-10 10:51:56.342 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-10 10:51:56.373 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000 May-10 10:51:56.676 [main] DEBUG nextflow.Session - Session start May-10 10:51:56.686 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/d/processing/quantms/results_lfq/pipeline_info/execution_trace_2023-05-10_10-51-55.txt May-10 10:51:56.712 [main] DEBUG nextflow.Session - Using default localLib path: /home/radu/.nextflow/assets/bigbio/quantms/lib May-10 10:51:56.718 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/radu/.nextflow/assets/bigbio/quantms/lib May-10 10:51:56.719 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/radu/.nextflow/assets/bigbio/quantms/lib/nfcore_external_java_deps.jar May-10 10:51:58.135 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-10 10:51:58.267 [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;35m nf-core/quantms v1.2.0dev-g7363d90[0m -[2m----------------------------------------------------[0m- [1mCore Nextflow options[0m [0;34mrevision : [0;32mdev[0m [0;34mrunName : [0;32minfallible_leibniz[0m [0;34mcontainerEngine : [0;32mdocker[0m [0;34mlaunchDir : [0;32m/mnt/d/processing/quantms[0m [0;34mworkDir : [0;32m/mnt/d/processing/quantms/work[0m [0;34mprojectDir : [0;32m/home/radu/.nextflow/assets/bigbio/quantms[0m [0;34muserName : [0;32mradu[0m [0;34mprofile : [0;32mtest_lfq,docker[0m [0;34mconfigFiles : [0;32m/home/radu/.nextflow/assets/bigbio/quantms/nextflow.config[0m [1mInput/output options[0m [0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design_urls.tsv[0m [0;34moutdir : [0;32m./results_lfq[0m [1mProtein database[0m [0;34mdatabase : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta[0m [0;34mdecoy_string : [0;32mrev[0m [1mDatabase search[0m [0;34msearch_engines : [0;32mmsgf,comet[0m [0;34minstrument : [0;32mnull[0m [1mModification localization[0m [0;34mluciphor_debug : [0;32m0[0m [1mPSM re-scoring (general)[0m [0;34mposterior_probabilities : [0;32mfit_distributions[0m [0;34mrun_fdr_cutoff : [0;32m0.10[0m [1mPSM re-scoring (Percolator)[0m [0;34mdescription_correct_features : [0;32m0[0m [1mConsensus ID[0m [0;34mconsensusid_considered_top_hits: [0;32m0[0m [0;34mmin_consensus_support : [0;32m0[0m [1mIsobaric analyzer[0m [0;34mselect_activation : [0;32mHCD[0m [1mProtein inference[0m [0;34mprotein_level_fdr_cutoff : [0;32m1.0[0m [0;34mpsm_level_fdr_cutoff : [0;32m1.0[0m [1mProtein Quantification (DDA)[0m [0;34mlabelling_type : [0;32mlabel free sample[0m [0;34mratios : [0;32mfalse[0m [0;34mnormalize : [0;32mfalse[0m [0;34mfix_peptides : [0;32mfalse[0m [1mProtein Quantification (LFQ)[0m [0;34mquantify_decoys : [0;32mtrue[0m [1mDIA-NN[0m [0;34mscan_window : [0;32m8[0m [1mStatistical post-processing[0m [0;34mcontrasts : [0;32mpairwise[0m [0;34madd_triqler_output : [0;32mtrue[0m [1mQuality control[0m [0;34menable_pmultiqc : [0;32mtrue[0m [1mInstitutional config options[0m [0;34mconfig_profile_name : [0;32mTest profile for DDA LFQ[0m [0;34mconfig_profile_description : [0;32mMinimal test dataset to check pipeline function of the label-free quantification branch of the pipeline[0m [1mMax job request options[0m [0;34mmax_cpus : [0;32m2[0m [0;34mmax_memory : [0;32m6 GB[0m [0;34mmax_time : [0;32m2d[0m [1mGeneric options[0m [0;34mhostnames : [0;32m[:][0m !! Only displaying parameters that differ from the pipeline defaults !! -[2m----------------------------------------------------[0m- If you use nf-core/quantms for your analysis please cite: * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/quantms/blob/master/CITATIONS.md -[2m----------------------------------------------------[0m- [ SNIPPED FOR LENGTH ] May-10 10:52:25.145 [Task submitter] INFO nextflow.Session - [37/0e705d] Submitted process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F1) May-10 10:52:26.445 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA1_F1); status: COMPLETED; exit: 9; error: -; workDir: /mnt/d/processing/quantms/work/34/a167ae569775aef72846217f704069] May-10 10:52:26.455 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA1_F1); work-dir=/mnt/d/processing/quantms/work/34/a167ae569775aef72846217f704069 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA1_F1)` terminated with an error exit status (9) May-10 10:52:26.470 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-10 10:52:26.472 [Task submitter] INFO nextflow.Session - [05/d4ff2a] Submitted process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA2_F1) May-10 10:52:26.490 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA1_F1)' Caused by: Process `NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA1_F1)` terminated with an error exit status (9) Command executed: CometAdapter \ -in BSA1_F1.mzML \ -out BSA1_F1_comet.idXML \ -threads 2 \ -database "18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta" \ -instrument high_res \ -missed_cleavages 2 \ -min_peptide_length 6 \ -max_peptide_length 40 \ -num_hits 1 \ -num_enzyme_termini fully \ -enzyme "Trypsin/P" \ -isotope_error 0/1 \ -precursor_charge 2:4 \ -fixed_modifications 'Carbamidomethyl (C)' \ -variable_modifications 'Oxidation (M)' \ -max_variable_mods_in_peptide 3 \ -precursor_mass_tolerance 5 \ -precursor_error_units ppm \ -fragment_mass_tolerance 0.03 \ -fragment_bin_offset 0.0 \ -PeptideIndexing:IL_equivalent \ -PeptideIndexing:unmatched_action warn \ -debug 0 \ -force \ \ 2>&1 | tee BSA1_F1_comet.log cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET": CometAdapter: $(CometAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1) Comet: $(comet 2>&1 | grep -E "Comet version.*" | sed 's/Comet version //g' | sed 's/"//g') END_VERSIONS Command exit status: 9 Command output: Standard output: Running: /usr/local/bin/comet.exe -P/tmp/20230510_175225_4e91810225f1_706_1/param.txt -N/tmp/20230510_175225_4e91810225f1_706_1/result BSA1_F1.mzML Comet version "2023.01 rev. 0" Standard error: Process '/usr/local/bin/comet.exe' crashed hard (segfault-like). Please check the log. CometAdapter took 0.37 s (wall), 0.19 s (CPU), 0.04 s (system), 0.15 s (user); Peak Memory Usage: 44 MB. Command error: Standard output: Running: /usr/local/bin/comet.exe -P/tmp/20230510_175225_4e91810225f1_706_1/param.txt -N/tmp/20230510_175225_4e91810225f1_706_1/result BSA1_F1.mzML Comet version "2023.01 rev. 0" Standard error: Process '/usr/local/bin/comet.exe' crashed hard (segfault-like). Please check the log. CometAdapter took 0.37 s (wall), 0.19 s (CPU), 0.04 s (system), 0.15 s (user); Peak Memory Usage: 44 MB. Work dir: /mnt/d/processing/quantms/work/34/a167ae569775aef72846217f704069 Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line May-10 10:52:26.505 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit May-10 10:52:26.521 [main] DEBUG nextflow.Session - Session await > all processes finished May-10 10:52:26.796 [Actor Thread 8] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 10; slices: 1; internal sort time: 0.24 s; external sort time: 0.003 s; total time: 0.243 s May-10 10:52:26.912 [Actor Thread 8] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/d/processing/quantms/work/collect-file/8945dc6bc58d7a555a7214bd5071616e May-10 10:52:26.920 [Actor Thread 8] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-12579009718896535592 May-10 10:52:28.485 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS (BSA2_F2); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/processing/quantms/work/dd/8317d868bf0ca75d4c7f1e5e50e994] May-10 10:52:29.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS (BSA3_F1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/processing/quantms/work/c2/7b7ca144b6ad6c3ef4ff6ae6228202] May-10 10:52:30.981 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA2_F1); status: COMPLETED; exit: 9; error: -; workDir: /mnt/d/processing/quantms/work/05/d4ff2a25bf10af30f7f67f1067772c] May-10 10:52:30.982 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA2_F1); work-dir=/mnt/d/processing/quantms/work/05/d4ff2a25bf10af30f7f67f1067772c error [nextflow.exception.ProcessFailedException]: Process `NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (BSA2_F1)` terminated with an error exit status (9) May-10 10:53:00.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA1_F1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/processing/quantms/work/74/86fb6b28a8c83dda9624b9286bc646] May-10 10:53:07.556 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/d/processing/quantms/work/37/0e705d9e33136485beb95687410588] May-10 10:53:07.624 [main] DEBUG nextflow.Session - Session await > all barriers passed May-10 10:53:07.665 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) May-10 10:53:07.668 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/quantms][0;31m Pipeline completed with errors[0m- May-10 10:53:07.673 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=15; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=9; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=2m 59s; failedDuration=19.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=5; peakCpus=10; peakMemory=30 GB; ] May-10 10:53:07.674 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file May-10 10:53:07.678 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report May-10 10:53:07.718 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":426,"min":426,"q1":426,"q2":426,"q3":426,"max":426,"minLabel":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","maxLabel":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","q1Label":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","q2Label":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","q3Label":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)"},"process":"SAMPLESHEET_CHECK","mem":{"mean":56684544,"min":56684544,"q1":56684544,"q2":56684544,"q3":56684544,"max":56684544,"minLabel":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","maxLabel":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","q1Label":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)","q2Label":"NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK 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(BSA1_F1)","q3Label":"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA1_F1)"},"writes":{"mean":50552374,"min":50266013,"q1":50409193.5,"q2":50552374,"q3":50695554.5,"max":50838735,"minLabel":"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA1_F1)","maxLabel":"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F1)","q1Label":"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA1_F1)","q2Label":"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA1_F1)","q3Label":"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA1_F1)"}}] May-10 10:53:08.400 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline May-10 10:53:08.637 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-10 10:53:08.677 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) May-10 10:53:08.682 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye ```

System information

Running on a Windows 10 workstation in a reasonably fresh Ubuntu 22.04 WSL2 environment.

Nextflow 23.04.1 build 5866 Container engine: Docker 23.0.5, build bc4487 WSL version: 1.1.3.0 Kernel version: 5.15.90.1

ypriverol commented 1 year ago

@radusuciu How much memory did you allocate in Docker?

radusuciu commented 1 year ago

I did not explicitly configure a system-wide memory limit for docker and to my knowledge there shouldn't be a limit (other than system memory) by default -- I did not approach the system memory limit, at least as reported by Task Manager. I did try adding a --memory-limit=16GB parameter but got the same error.

I should also note that I've verified that comet itself runs fine on WSL2. I have not however tested CometAdapter by itself (ie. not as a part of quantms)

ypriverol commented 1 year ago

Sorry to bother you. Can you try conda?

jpfeuffer commented 1 year ago

Or did you try running comet from docker inside WSL2 e.g. by pulling and starting its biocontainer or openms-thirdparty biocontainer?

radusuciu commented 1 year ago

Sorry to bother you. Can you try conda?

Not a bother at all - happy to provide more information! Just a few notes on the conda installation process starting from a fresh install of conda:

I needed to add bioconda and conda-forge channels: conda config --add channels bioconda, conda config --add channels conda-forge
I needed to install mamba: conda install -c conda-forge mamba

After those steps, I was able to run the following command: ./nextflow run bigbio/quantms -r dev -profile test_lfq,conda which after a long time crashed before reaching the comet step. I ran it again and it seems like I also need OpenMS installed locally outside of conda so I will do that and report back.

Or did you try running comet from docker inside WSL2 e.g. by pulling and starting its biocontainer or openms-thirdparty biocontainer?

I do this all the time but not with the biocontainer or openms-thirdparty container -- I will try this as well.

jpfeuffer commented 1 year ago

Thanks for trying.

Regarding conda, openms should come with it as well (in the bioconda channel). There probably was something wrong during installation of the packages.

To clarify on docker: If you use the docker profile, it will pull the openms-thirdparty biocontainer, which is based on the bioconda builds for every step that involves openms or an openms adapter. It includes both openms and most third-party tools. The inclusion is done by just referencing a specific conda version of the thirdparties (in this case comet-ms). Therefore the binaries you get should be the same if you use comet-ms or openms-thirdparty biocontainer. They actually should be even the same as with the conda profile (as long as the WSL has the same architecture as the biocontainers, which it should). The only difference is the additional layer of "containerization", in this case level 3, since WSL alone is already a "container".

radusuciu commented 1 year ago

So I went on a quick debugging journey which you can follow below. My conclusion is that docker is a red herring in this case, and that this isn't related to quantms at all. However, it does seem to be related to the comet binary that is distributed with the openms container. There was no issue when using the latest comet binary from the comet repo (or any of them for that matter) or from the OpenMS/THIRDPARTY repo, so it seems that the issue lies with the binary being distributed with the quay.io/biocontainers/openms-thirdparty:2.9.1--h9ee0642_1 image.

My debugging journey

Alright, now we're getting closer. I can reproduce the issue when running the comet binary in the openms-thirdparty container. This I think means that this issue is not really related to quantms.

$ docker run -it --rm -v $PWD:/data quay.io/biocontainers/openms-thirdparty:2.9.1--h9ee0642_1 comet -P/data/comet.params.new -D/data/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta /data/BSA1_F1.mzML

and in the host /var/sys/log:

May 11 14:32:06 US320024WSD kernel: [173790.615518] comet[3747012] vsyscall attempted with vsyscall=none ip:ffffffffff600400 cs:33 sp:7fff1e2f41b8 ax:ffffffffff600400 si:2e di:0
May 11 14:32:06 US320024WSD kernel: [173790.615525] comet[3747012]: segfault at ffffffffff600400 ip ffffffffff600400 sp 00007fff1e2f41b8 error 15
May 11 14:32:06 US320024WSD kernel: [173790.615529] Code: Unable to access opcode bytes at RIP 0xffffffffff6003d6.
May 11 14:32:06 US320024WSD kernel: [173790.615535] potentially unexpected fatal signal 11.
May 11 14:32:06 US320024WSD kernel: [173790.615536] CPU: 18 PID: 3747012 Comm: comet Not tainted 5.15.90.1-microsoft-standard-WSL2 #1
May 11 14:32:06 US320024WSD kernel: [173790.615539] RIP: 0033:0xffffffffff600400
May 11 14:32:06 US320024WSD kernel: [173790.615543] Code: Unable to access opcode bytes at RIP 0xffffffffff6003d6.
May 11 14:32:06 US320024WSD kernel: [173790.615544] RSP: 002b:00007fff1e2f41b8 EFLAGS: 00010206
May 11 14:32:06 US320024WSD kernel: [173790.615546] RAX: ffffffffff600400 RBX: 0000000000000054 RCX: 0000000000000010
May 11 14:32:06 US320024WSD kernel: [173790.615548] RDX: 0000000000000000 RSI: 000000000000002e RDI: 0000000000000000
May 11 14:32:06 US320024WSD kernel: [173790.615549] RBP: 00007fff1e2f4240 R08: 000000000082b5e0 R09: 0000000000000000
May 11 14:32:06 US320024WSD kernel: [173790.615550] R10: 403202b45e40fdf7 R11: 0000000000000206 R12: 00007fff1e2f4340
May 11 14:32:06 US320024WSD kernel: [173790.615551] R13: 00007fff1e2f4308 R14: 000000000082b5e0 R15: 00007fff1e2f4350
May 11 14:32:06 US320024WSD kernel: [173790.615553] FS:  0000000001265880 GS:  0000000000000000

Let's do some sanity checks and try some stuff

1. Download latest comet.linux.exe binary from the comet github page, rename to comet and run in WSL:

$ ./comet -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1.mzML
 Comet version "2023.01 rev. 2 (7c9150d)"

 Search start:  05/11/2023, 02:44:48 PM
 - Input file: BSA1_F1.mzML
   - Load spectra: 481
     - Search progress: 100%
     - Post analysis:  done
 Search end:    05/11/2023, 02:44:51 PM, 0m:3s

Okay, that works well enough.

2. Let's do the same, but in a Ubuntu container

$ docker run -it --rm -v $PWD:/data ubuntu /data/comet -P/data/comet.params.new -D/data/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta /data/BSA1_F1.mzML
 Comet version "2023.01 rev. 2 (7c9150d)"

 Search start:  05/11/2023, 09:48:40 PM
 - Input file: /data/BSA1_F1.mzML
   - Load spectra: 481
     - Search progress: 100%
     - Post analysis:  done
 Search end:    05/11/2023, 09:48:43 PM, 0m:3s

Okay, so that works too.. I also tried different versions of Ubuntu and those all worked too.

3. Alright, let's swap in the OpenMS comet binary from the OpenMS/THIRDPARTY repo

Let's confirm it's based on the same comet release.

$ wget -q https://github.com/OpenMS/THIRDPARTY/raw/master/Linux/64bit/Comet/comet.exe -O comet_openms && ./comet_openms

 Comet version 2023.01 rev. 2 (7c9150d)

okay good, now let's run it locally:

$ ./comet_openms -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1.mzML
 Comet version "2023.01 rev. 2 (7c9150d)"

 Search start:  05/11/2023, 03:00:57 PM
 - Input file: BSA1_F1.mzML
   - Load spectra: 481
     - Search progress: 100%
     - Post analysis:  done
 Search end:    05/11/2023, 03:00:59 PM, 0m:2s

okay, that works, now lets run the openms binary inside an ubuntu container as we did before:

$ docker run -it --rm -v $PWD:/data ubuntu /data/comet_openms -P/data/comet.params.new -D/data/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta /data/BSA1_F1.mzML
 Comet version "2023.01 rev. 2 (7c9150d)"

 Search start:  05/11/2023, 10:01:49 PM
 - Input file: /data/BSA1_F1.mzML
   - Load spectra: 481
     - Search progress: 100%
     - Post analysis:  done
 Search end:    05/11/2023, 10:01:52 PM, 0m:3s

so that works just fine... however. I noticed that it's not the same binary, so let's copy it from the container directly:

 $ docker cp fe2b26f4027e:/usr/local/bin/comet comet_openms_container
Successfully copied 11.1MB to /mnt/d/processing/quantms/comet_openms_container

and then run it in WSL2 directly:

$ ./comet_openms_container -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1.mzML
Segmentation fault

and in an ubuntu container:

$ docker run -it --rm -v $PWD:/data ubuntu /data/comet_openms_container -P/data/comet.params.new -D/data/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta /data/BSA1_F1.mzML

no output, and the same failed vsyscall is logged in the host (WSL2) /var/log/syslog.

4. Let's try a bunch of different comet binaries, forgetting about docker since it doesn't seem to be relevant.

VERSION=2021.02.0; wget -q https://github.com/UWPR/Comet/releases/download/v${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1.mzML
VERSION=2022.01.0; wget -q https://github.com/UWPR/Comet/releases/download/v${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1.mzML

# here I indexed the mzML file since Comet removed and later re-added support regular mzMLs
VERSION=2022.01.1; wget -q https://github.com/UWPR/Comet/releases/download/v${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1_indexed.mzML
VERSION=2022.01.2; wget -q https://github.com/UWPR/Comet/releases/download/v${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1_indexed.mzML
VERSION=2023.01.0; wget -q https://github.com/UWPR/Comet/releases/download/v${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1_indexed.mzML

# note this one had a slightly different version string... V instead of v
VERSION=2023.01.1; wget -q https://github.com/UWPR/Comet/releases/download/V${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1_indexed.mzML

# back to regular mzML
VERSION=2023.01.2; wget -q https://github.com/UWPR/Comet/releases/download/v${VERSION}/comet.linux.exe -O comet${VERSION} && ./comet${VERSION} -p && ./comet${VERSION} -Pcomet.params.new -D18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta BSA1_F1.mzML

They all run fine (once we use a indexed BSA_F1.mzML for versions that require it) so it seems that the issue is with the binary being distributed with the quay.io/biocontainers/openms-thirdparty:2.9.1--h9ee0642_1 image.

jpfeuffer commented 1 year ago

Cool. That is helpful. Searching for the segfault I found: https://github.com/rancher-sandbox/rancher-desktop/issues/2215

Specifically with the comment https://github.com/microsoft/WSL/issues/4694#issuecomment-556095344

You could try that. Would be better to fix this during the bioconda build but not sure if it requires changes in the bioconda buildsystem/pinned versions of GCC/glibc or in the comet recipe or the comet code itself.

radusuciu commented 1 year ago

Yep, the comment you linked makes it work, specifically, adding:

[wsl2]
kernelCommandLine = vsyscall=emulate

to %userprofile%\.wslconfig (creating the file if it does not exist already). Now we can run comet in the openms-thirdparty biocontainer just fine:

$ docker run -it --rm -v $PWD:/data quay.io/biocontainers/openms-thirdparty:2.9.1--h9ee0642_1 comet -P/data/comet.params.new -D/data/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta /data/BSA1_F1_indexed.mzML
 Comet version "2023.01 rev. 0"

 Search start:  05/11/2023, 11:04:47 PM
 - Input file: /data/BSA1_F1_indexed.mzML
   - Load spectra: 481
     - Search progress: 100%
     - Post analysis:  done
 Search end:    05/11/2023, 11:04:49 PM, 0m:2s

and ./nextflow run bigbio/quantms -r dev -profile test_lfq also works! Thanks for the help! Hopefully this is a good workaround for others using WSL2 (there are dozens of us!).

jpfeuffer commented 1 year ago

Very nice. I always wanted to try myself as well on WSL. Thanks a lot.

We could add a note in the "Run" section of the docs or a new "Known issues" section of the docs/changelog.

We could also forward to bioconda (@ypriverol often does updates of conda recipes). From the short look in the linked issues, I have the feeling this could be avoided by not statically linking to glibc in the comet bioconda recipe, but I am not sure.

ypriverol commented 1 year ago

Also to the readthedocs section known issues, we should update it.

ypriverol commented 10 months ago

Stale issue, close for now, please reopen if needed.

bigbio / quantms