error exit status (139) during ARROW_02:merge_consensus in the Case I run

[junesk9]

Hi,

I really thank to you all for this one-step polishing tool of an easy-use.
My current assembly is for an algal species, trying to process a Canu (v2.2) assembly as the Case I.

The latest polishCLR is set-up on a local Ubuntu 22.04 system by nextflow (23.04.1.586) and conda (23.3.1) with the .yml file owing to your guidance.

The command I used is like below.

nextflow run isugifNF/polishCLR -r main --primary_assembly "asm.contigs.fasta" --illumina_reads "PE..fq.gz" --pacbio_reads "m.bam" --step 1 --falcon_unzip false -resume -latest

The run was terminated at the "process > ARROW_02:merge_consensus" stage with following error massage.

May-24 09:31:02.345 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-24 09:31:02.347 [Task submitter] INFO nextflow.Session - [73/61bd41] Submitted process > ARROW_02:merge_consensus (1)
May-24 09:31:03.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26931; name: >ARROW_02:merge_consensus (1); status: COMPLETED; exit: 139; error: -; workDir: /home/gdrg1/data/labor3/21_polishCLR/work/73/61bd410320c4ccf58791c88254687e]
May-24 09:31:03.062 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=ARROW_02:merge_consensus (1); work-dir=/home/gdrg1/data/labor3/21_polishCLR/work/73/61bd410320c4ccf58791c88254687e
error [nextflow.exception.ProcessFailedException]: Process ARROW_02:merge_consensus (1) terminated with an error exit status (139)
May-24 09:31:03.084 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: /home/gdrg1/data/labor3/21_polishCLR/work/73/61bd410320c4ccf58791c88254687e/.command.out
May-24 09:31:03.085 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: /home/gdrg1/data/labor321_polishCLR/work/73/61bd410320c4ccf58791c88254687e/.command.err
May-24 09:31:03.093 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'ARROW_02:merge_consensus (1)'

Caused by:
Process ARROW_02:merge_consensus (1) terminated with an error exit status (139)

Command executed:

#! /usr/bin/env bash
OUTNAME=echo "Step_1/01_ArrowPolish" | sed 's:/:_:g'
cat species_name_assembly_pri_tig00000007_0-36040.fasta species_name_assembly_pri_tig00000003_0-44741.fasta
..... (skip; it a quite length of files listed) ... 9568.fasta > ${OUTNAME}_consensus.fasta
Command exit status:
139

Command output:
(empty)

Work dir:
/home/gdrg1/data/labor3/21_polishCLR/work/73/61bd410320c4ccf58791c88254687e

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

So I visited the work path, and found the path lacks of any fasta file which neighbor paths have,
and excute the .command.run output the "core dump segment error".

I hope you may have any advice for this trouble.