Unable to dump output of process 'xxx' -- Cause: java.nio.file.NoSuchFileException .command.out/.command.err #3981

Tong-Chen · 2023-05-28T07:30:42Z

Tong-Chen
May 28, 2023

I have a workflow RNAseq_salmon.nf, which could be run successfully in bash terminal manually in /path or through python module subprocess (based on Popen(RNAseq_salmon.nf, cwd="/path")). However, when running this process using Celery (which also uses Popen to run (RNAseq_salmon.nf internally), it fails.

The most explicit error is:

May-26 19:13:44.820 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: SALMON_QUANT (trt_N061011); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a]
May-26 19:13:44.837 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'SALMON_QUANT (trt_N061011)' -- Unable to dump output of process Cause: java.nio.file.NoSuchFileException .command.out: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.out
May-26 19:13:44.838 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'SALMON_QUANT (trt_N061011)' -- Cause: java.nio.file.NoSuchFileException: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.err

When I move to the directory /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/ and run bash .command.run, it finished successfully.

Normally when I met java.nio.file.NoSuchFileException, it may be caused by the parent directory being uncreated. I wonder if there is one possibility that when dumping errors to .command.out, the dir work/b3/27c8e1eef9a76d2ba053753bb88d0a is missing. But when I check the errors, these directories are ready. I just do not know why.

Also, it is weird, since .command.run is generated, which means the directory work/b3/27c8e1eef9a76d2ba053753bb88d0a is created.

I have tried to change workDir to another directory and searched using Google and got no luck.

Could anyone please give some suggestions?

Thanks!

Chen Tong

Full logs below:

May-26 19:13:33.835 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.04.5

May-26 19:13:36.263 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/bogon/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
May-26 19:13:36.266 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
May-26 19:13:36.293 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-26 19:13:36.295 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-26 19:13:36.304 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
May-26 19:13:36.326 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
May-26 19:13:36.452 [main] DEBUG nextflow.Session - Session uuid: 3c7f7171-96b7-418f-b6c6-4689ecfd822b
May-26 19:13:36.452 [main] DEBUG nextflow.Session - Run name: disturbed_saha
May-26 19:13:36.453 [main] DEBUG nextflow.Session - Executor pool size: 80
May-26 19:13:36.538 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 22.04.5 build 5708
  Created: 15-07-2022 16:09 UTC (16-07-2022 00:09 CDT)
  System: Linux 4.18.0-305.10.2.el8_4.x86_64
  Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 17.0.4+8
  Encoding: UTF-8 (UTF-8)
  Process: 2791252@bogon [192.168.0.102]
  CPUs: 80 - Mem: 361.8 GB (299.7 GB) - Swap: 119.2 GB (88.7 GB)
May-26 19:13:36.597 [main] DEBUG nextflow.Session - Work-dir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work [ext2/ext3]
May-26 19:13:36.598 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/bogon/bin/bin
May-26 19:13:36.631 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
May-26 19:13:36.652 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-26 19:13:36.751 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-26 19:13:36.771 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
May-26 19:13:36.902 [main] DEBUG nextflow.Session - Session start invoked
May-26 19:13:36.909 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/ed9908ef-89d6-4b91-b379-d159deb19f96/pipeline_info/execution_trace.txt
May-26 19:13:37.457 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-26 19:13:39.017 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name SALMON_QUANT
May-26 19:13:39.033 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-26 19:13:39.034 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-26 19:13:39.046 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
May-26 19:13:39.061 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=361.8 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
May-26 19:13:39.215 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1, 2]
May-26 19:13:39.272 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name SALMON_QUANT_OUTPUT
May-26 19:13:39.274 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-26 19:13:39.274 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-26 19:13:39.300 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name SALMON_QUANT_DE
May-26 19:13:39.307 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-26 19:13:39.307 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-26 19:13:39.328 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: SALMON_QUANT_DE, SALMON_BUILD_INDEX, SALMON_QUANT_OUTPUT, SALMON_QUANT, SALMON_QUANT_OUTPUT_INNER
May-26 19:13:39.330 [main] DEBUG nextflow.Session - Ignite dataflow network (9)
May-26 19:13:39.346 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SALMON_QUANT
May-26 19:13:39.348 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SALMON_QUANT
May-26 19:13:39.349 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SALMON_QUANT_OUTPUT
May-26 19:13:39.352 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SALMON_QUANT_DE
May-26 19:13:39.354 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
May-26 19:13:39.354 [main] DEBUG nextflow.Session - Session await
May-26 19:13:39.614 [Actor Thread 41] DEBUG nextflow.conda.CondaCache - conda found local env for environment=/anaconda3/envs/transcriptome/; path=/anaconda3/envs/transcriptome
May-26 19:13:39.822 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.832 [Task submitter] INFO  nextflow.Session - [18/bc1037] Submitted process > SALMON_QUANT (untrt_N052611)
May-26 19:13:39.851 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.852 [Task submitter] INFO  nextflow.Session - [fb/7681de] Submitted process > SALMON_QUANT (trt_N080611)
May-26 19:13:39.874 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.875 [Task submitter] INFO  nextflow.Session - [b2/5fcc5a] Submitted process > SALMON_QUANT (untrt_N61311)
May-26 19:13:39.893 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.893 [Task submitter] INFO  nextflow.Session - [b3/3d236c] Submitted process > SALMON_QUANT (trt_N052611)
May-26 19:13:39.909 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.910 [Task submitter] INFO  nextflow.Session - [18/250c6b] Submitted process > SALMON_QUANT (trt_N61311)
May-26 19:13:39.928 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.929 [Task submitter] INFO  nextflow.Session - [b3/27c8e1] Submitted process > SALMON_QUANT (trt_N061011)
May-26 19:13:39.947 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.948 [Task submitter] INFO  nextflow.Session - [56/e85c69] Submitted process > SALMON_QUANT (untrt_N061011)
May-26 19:13:39.967 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-26 19:13:39.968 [Task submitter] INFO  nextflow.Session - [ba/4516b7] Submitted process > SALMON_QUANT (untrt_N080611)
May-26 19:13:44.820 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: SALMON_QUANT (trt_N061011); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a]
May-26 19:13:44.837 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'SALMON_QUANT (trt_N061011)' -- Unable to dump output of process Cause: java.nio.file.NoSuchFileException .command.out: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.out
May-26 19:13:44.838 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'SALMON_QUANT (trt_N061011)' -- Cause: java.nio.file.NoSuchFileException: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.err
May-26 19:13:44.851 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'SALMON_QUANT (trt_N061011)'

Caused by:
  Process `SALMON_QUANT (trt_N061011)` terminated with an error exit status (1)

Command executed:

  mkdir -p trt_N061011
  salmon quant --gcBias -l A -i GRCh38.salmon.index \
        -1 trt_N061011_1.fq.gz -2 trt_N061011_2.fq.gz -o trt_N061011 -p 6  -g Genome.gtf

Command exit status:
  1

Command output:
  (empty)

Work dir:
  /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a

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`
May-26 19:13:44.880 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
May-26 19:13:44.889 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'SALMON_QUANT (trt_N061011)' -- Cause: java.nio.file.NoSuchFileException: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.err
May-26 19:13:44.889 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'SALMON_QUANT (trt_N061011)' -- Cause: java.nio.file.NoSuchFileException: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.out
May-26 19:13:44.891 [main] DEBUG nextflow.Session - Session await > all process finished
May-26 19:13:44.893 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: SALMON_QUANT (untrt_N061011); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/56/e85c6970c58ecd820fbc274593ce7f]
May-26 19:13:44.896 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: SALMON_QUANT (untrt_N080611); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/ba/4516b78775022bd715671cc3b90255]
May-26 19:13:44.901 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: SALMON_QUANT (trt_N61311); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/18/250c6b06bbaad24d9a75715210e86c]
May-26 19:13:45.017 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: SALMON_QUANT (untrt_N052611); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/18/bc10379d7cf01633e064ab8016612b]
May-26 19:13:45.115 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: SALMON_QUANT (untrt_N61311); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b2/5fcc5adb76a8a372a84f8d466a7fd7]
May-26 19:13:45.703 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: SALMON_QUANT (trt_N080611); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/fb/7681dea42dfcdef5dbb14c9bb6c951]
May-26 19:13:45.715 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: SALMON_QUANT (trt_N052611); status: COMPLETED; exit: 1; error: -; workDir: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/3d236c746f31895d05fcbfb7156232]
May-26 19:13:45.723 [main] DEBUG nextflow.Session - Session await > all barriers passed
May-26 19:13:45.725 [main] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'SALMON_QUANT (trt_N061011)' -- Cause: java.nio.file.NoSuchFileException: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.err
May-26 19:13:45.726 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'SALMON_QUANT (trt_N061011)' -- Cause: java.nio.file.NoSuchFileException: /fidRNAseq_analysis_flow__salmon_50002023_05_26_19_13_31_621799/work/b3/27c8e1eef9a76d2ba053753bb88d0a/.command.out
May-26 19:13:45.738 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=8; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=4m 8s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=8; peakCpus=48; peakMemory=288 GB; ]
May-26 19:13:45.738 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
May-26 19:13:45.742 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
May-26 19:13:45.824 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"SALMON_QUANT","mem":null,"memUsage":null,"timeUsage":{"mean":0.02,"min":0.02,"q1":0.02,"q2":0.02,"q3":0.02,"max":0.02,"minLabel":"SALMON_QUANT (trt_N061011)","maxLabel":"SALMON_QUANT (trt_N080611)","q1Label":"SALMON_QUANT (untrt_N080611)","q2Label":"SALMON_QUANT (trt_N61311)","q3Label":"SALMON_QUANT (untrt_N61311)"},"vmem":null,"reads":null,"cpu":null,"time":{"mean":5172.75,"min":4810,"q1":4889.25,"q2":5020.5,"q3":5343.75,"max":5809,"minLabel":"SALMON_QUANT (trt_N061011)","maxLabel":"SALMON_QUANT (trt_N080611)","q1Label":"SALMON_QUANT (untrt_N080611)","q2Label":"SALMON_QUANT (trt_N61311)","q3Label":"SALMON_QUANT (untrt_N61311)"},"writes":null}]
May-26 19:13:46.979 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
May-26 19:13:47.102 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
May-26 19:13:47.121 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

bentsherman · 2023-05-31T14:21:57Z

bentsherman
May 31, 2023
Maintainer

The error about the out/err files is usually a red herring, i.e. it's usually just a consequence of some upstream error. In this case, it looks like the task failed because it returned exit code 1. I would look into what that is happening.

0 replies

Tong-Chen · 2023-06-02T07:14:43Z

Tong-Chen
Jun 2, 2023
Author

I have set debug=true and got no error log info. And I got no out/err files. Is there another way to check the log of exit code 1?

Additionally, I tried to run bash .command.run in b3/27c8e1eef9a76d2ba053753bb88d0a and got success.

4 replies

bentsherman Jun 2, 2023
Maintainer

Did you get a .command.log file? And when you ran the script manually, did you get out/err files?

Tong-Chen Jun 2, 2023
Author

Yes. I get an empty .commad.log; 2. When I run the script manually, I get out/err file.

bentsherman Jun 2, 2023
Maintainer

My suspicion is that something is failing in the .command.run, but if you can run it manually just fine then I'm not sure. Does it fail when you run it with Nextflow? Or only when you run it with Celery + Nextflow?

I would also try the latest stable release, 23.04, because there have been a ton of bug fixes in the past year.

Tong-Chen Jun 2, 2023
Author

It only fails when Celery + Nextflow. That is the weirdest part. In celery, I used subprocess.popen to run nextflow.

I can get it to work if I directly run subprocess.popen("nextflow xxxx") under the python interactive shell.
I can get it to work in bash terminal nxtflow xxxx also.

Tong-Chen · 2023-06-02T10:57:04Z

Tong-Chen
Jun 2, 2023
Author

Sorry for the misleading. I have updated Nextflow (23.04) to the latest version and the specified java version (Temurin 17) (after I post the first logs in this question).

I may found the cause but still do not know why. The error is supposed to be caused by the activation of conda environment.

When the process is defined as below, it gets wrong:

process SALMON_QUANT {
    conda "/anaconda3/envs/transcriptome/"

   script:
        def reference   = "-i ${Salmon_index}"
        def input_reads = meta.single_end ? "-r ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
        def gene_level = genome_gtf.name == "Virtual_FiLE" ?  "" : " -g ${genome_gtf} "
        """
        mkdir -p ${meta.id}
        salmon quant --gcBias -l A $reference \\
              $input_reads -o ${meta.id} -p $task.cpus ${gene_level}
        """

When the process is defined as below, it gets right:

process SALMON_QUANT {
    // conda "/anaconda3/envs/transcriptome/"

   script:
        def reference   = "-i ${Salmon_index}"
        def input_reads = meta.single_end ? "-r ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
        def gene_level = genome_gtf.name == "Virtual_FiLE" ?  "" : " -g ${genome_gtf} "
        """
        mkdir -p ${meta.id}
       conda run -p "/anaconda3/envs/transcriptome/" salmon quant --gcBias -l A $reference \\
              $input_reads -o ${meta.id} -p $task.cpus ${gene_level}
        """

I noticed in .command.run, there is one script to activate conda environment source $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }')/bin/activate /anaconda3/envs/transcriptome. I checked the return of $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }') under nextflow, which is right /anaconda3.

I guess it may be caused by :

conda activate environment gets wrong.
.commd.run script stoped.
Then our/err file handler not found error.
But why the conda activate environment error message could not be captured in .command.log?

# 
source $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }')/bin/activate /anaconda3/envs/transcriptome
    set -u
    export PATH="./bin:${PATH}"
    [[ $NXF_SCRATCH ]] && echo "nxf-scratch-dir $HOSTNAME:$NXF_SCRATCH" && cd $NXF_SCRATCH
    nxf_stage

    set +e
    ctmp=$(set +u; nxf_mktemp /dev/shm 2>/dev/null || nxf_mktemp $TMPDIR)
    local cout=$ctmp/.command.out; mkfifo $cout
    local cerr=$ctmp/.command.err; mkfifo $cerr

1 reply

bentsherman Jun 2, 2023
Maintainer

Not sure, I know about Celery but never used it so I don't know how it executes tasks. I wonder if there is some conflict between the Celery environment and the conda environment used by this process.

Can you try the latest edge release, 23.05.0-edge? There are a few more bug fixes in there, one of them might be relevant. You can also do nextflow -trace nextflow run ... to enable trace logging, which might give you a few more helpful log messages...

Tong-Chen · 2023-06-02T13:13:53Z

Tong-Chen
Jun 2, 2023
Author

Thanks!

I have tried adding -trace but found no hints.
I have tested the conda activation command and found no errors.

process SALMON_QUANT {
    // conda "/anaconda3/envs/transcriptome/"

   script:
        def reference   = "-i ${Salmon_index}"
        def input_reads = meta.single_end ? "-r ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
        def gene_level = genome_gtf.name == "Virtual_FiLE" ?  "" : " -g ${genome_gtf} "
        """
        testconda.sh
        """

In testconda.sh:

source $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }')/bin/activate /anaconda3/envs/transcriptome >>/tmp/testcondalog  2>&1
echo $?  >>/tmp/testcondalog  2>&1

which conda >>/tmp/testcondalog  2>&1

In /tmp/testcondalog

0
/root/anaconda3/condabin/conda

I would try to update to the edge version later.

0 replies

Matt-BF · 2024-08-31T03:15:44Z

Matt-BF
Aug 31, 2024

Hi, I've encountered the same problem and @Tong-Chen 's conda hypothesis made me look deeper into my stack. I am using nextflow installed via a pixi environment. I was running my pipeline inside a pixi shell, which was erroring with "Unable to dump process". After exiting this shell and running the pipeline with pixi run instead, the pipeline completed flawlessly. So I guess this env activation issue might be a good place to investigate further

0 replies

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Unable to dump output of process 'xxx' -- Cause: java.nio.file.NoSuchFileException .command.out/.command.err #3981

Tong-Chen May 28, 2023

Replies: 5 comments · 5 replies

bentsherman May 31, 2023 Maintainer

Tong-Chen Jun 2, 2023 Author

bentsherman Jun 2, 2023 Maintainer

Tong-Chen Jun 2, 2023 Author

bentsherman Jun 2, 2023 Maintainer

Tong-Chen Jun 2, 2023 Author

Tong-Chen Jun 2, 2023 Author

bentsherman Jun 2, 2023 Maintainer

Tong-Chen Jun 2, 2023 Author

Matt-BF Aug 31, 2024

Tong-Chen
May 28, 2023

Replies: 5 comments 5 replies

bentsherman
May 31, 2023
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Tong-Chen
Jun 2, 2023
Author

bentsherman Jun 2, 2023
Maintainer

Tong-Chen Jun 2, 2023
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bentsherman Jun 2, 2023
Maintainer

Tong-Chen Jun 2, 2023
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Tong-Chen
Jun 2, 2023
Author

bentsherman Jun 2, 2023
Maintainer

Tong-Chen
Jun 2, 2023
Author

Matt-BF
Aug 31, 2024