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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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osx arm64/v8 failure on profile test,docker #1448

Open PikalaxALT opened 2 weeks ago

PikalaxALT commented 2 weeks ago

Description of the bug

STAR command fails to produce output in linux/amd64 mode on macOS arm64/v8 in docker profile

Command used and terminal output

% nextflow run nf-core/rnaseq -profile rnaseq,docker -process.containerOptions "--platform linux/amd64"

...

Execution cancelled -- Finishing pending tasks before exit -[nf-core/rnaseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)'

Caused by: Missing output file(s) *Log.final.out expected by process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)

Command executed:

STAR \ --genomeDir star \ --readFilesIn input1/RAP1_IAA_30M_REP1_primary_1.fastq.gz input2/RAP1_IAA_30M_REP1_primary_2.fastq.gz \ --runThreadN 4 \ --outFileNamePrefix RAP1_IAA_30M_REP1. \ \ --sjdbGTFfile genome_gfp.gtf \ --outSAMattrRGline 'ID:RAP1_IAA_30M_REP1' 'SM:RAP1_IAA_30M_REP1' \ --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantTranscriptomeSAMoutput BanSingleEnd

if [ -f RAP1_IAA_30M_REP1.Unmapped.out.mate1 ]; then mv RAP1_IAA_30M_REP1.Unmapped.out.mate1 RAP1_IAA_30M_REP1.unmapped_1.fastq gzip RAP1_IAA_30M_REP1.unmapped_1.fastq fi if [ -f RAP1_IAA_30M_REP1.Unmapped.out.mate2 ]; then mv RAP1_IAA_30M_REP1.Unmapped.out.mate2 RAP1_IAA_30M_REP1.unmapped_2.fastq gzip RAP1_IAA_30M_REP1.unmapped_2.fastq fi

cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STARALIGN": star: $(STAR --version | sed -e "s/STAR//g") samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//') gawk: $(echo $(gawk --version 2>&1) | sed 's/^.GNU Awk //; s/, .$//') END_VERSIONS

Command exit status: 0

Command output: (empty)

Work dir: /Users/pikalaxalt/nextflow-launch-directories/work/d2/c757228cbe86dafe7412bc3d1afd2d

Container: quay.io/nf-core/star_samtools_htslib_gawk:10c6e8c834460019

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

Relevant files

Version: 24.10.0 build 5928 Created: 27-10-2024 18:36 UTC (14:36 EDT) System: Mac OS X 15.1 Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21 Encoding: UTF-8 (UTF-8)

Core Nextflow options revision : master runName : serene_bhabha containerEngine : docker launchDir : /Users/pikalaxalt/nextflow-launch-directories workDir : /Users/pikalaxalt/nextflow-launch-directories/work projectDir : /Users/pikalaxalt/.nextflow/assets/nf-core/rnaseq userName : pikalaxalt profile : docker,test configFiles :

nextflow version: 24.10.0 hardware: macbook executor: local container engine: docker os: macos 15.1 silicon (arm64 v8) version of nf-core/rnaseq: 00f924cf92a986a842bb352b3c4ae379c773c989

System information

No response