Adding cellrangermulti subworkflow #874
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failed
Apr 8, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
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Check failure on line 1 in test-dataset_cellrangermulti_aligner
github-actions / JUnit Test Report
test-dataset_cellrangermulti_aligner
Assertion failed:
14 of 15 assertions failed
Raw output
Nextflow stdout:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.chromosome.2.fa)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.chromosome.2.fa)` terminated with an error exit status (1)
Command executed:
cellranger \
mkref \
--genome=gex_reference \
--fasta=Homo_sapiens.GRCh38.dna.chromosome.2.fa \
--genes=Homo_sapiens.GRCh38.dna.chromosome.2_genes.filtered.gtf \
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MKREF":
cellranger: $(echo $( cellranger --version 2>&1) | sed 's/^.*[^0-9]\([0-9]*\.[0-9]*\.[0-9]*\).*$/\1/' )
END_VERSIONS
Command exit status:
1
Command output:
['/opt/cellranger-7.1.0/bin/rna/mkref', '--genome=gex_reference', '--fasta=Homo_sapiens.GRCh38.dna.chromosome.2.fa', '--genes=Homo_sapiens.GRCh38.dna.chromosome.2_genes.filtered.gtf']
Apr 08 10:35:38 ..... started STAR run
Apr 08 10:35:38 ... starting to generate Genome files
Apr 08 10:35:44 ... starting to sort Suffix Array. This may take a long time...
Apr 08 10:35:45 ... sorting Suffix Array chunks and saving them to disk...
Creating new reference folder at gex_reference
...done
Writing genome FASTA file into reference folder...
...done
Indexing genome FASTA file...
...done
Writing genes GTF file into reference folder...
...done
Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
Failed to make genome index with STAR. This can occasionally be caused by setting the argument `memgb` too low.
Error was from running command '/opt/cellranger-7.1.0/lib/bin/STAR'
Command '['/opt/cellranger-7.1.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', 'gex_reference/star', '--runThreadN', '1', '--genomeFastaFiles', 'gex_reference/fasta/genome.fa', '--sjdbGTFfile', 'gex_reference/genes/genes.gtf', '--limitGenomeGenerateRAM', '17179869184', '--genomeSAsparseD', '1', '--genomeSAindexNbases', '12', '--genomeChrBinNbits', '18']' died with <Signals.SIGKILL: 9>.
Check stdout and stderr for more information.
Command error:
['/opt/cellranger-7.1.0/bin/rna/mkref', '--genome=gex_reference', '--fasta=Homo_sapiens.GRCh38.dna.chromosome.2.fa', '--genes=Homo_sapiens.GRCh38.dna.chromosome.2_genes.filtered.gtf']
Apr 08 10:35:38 ..... started STAR run
Apr 08 10:35:38 ... starting to generate Genome files
Apr 08 10:35:44 ... starting to sort Suffix Array. This may take a long time...
Apr 08 10:35:45 ... sorting Suffix Array chunks and saving them to disk...
Creating new reference folder at gex_reference
...done
Writing genome FASTA file into reference folder...
...done
Indexing genome FASTA file...
...done
Writing genes GTF file into reference folder...
...done
Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
Failed to make genome index with STAR. This can occasionally be caused by setting the argument `memgb` too low.
Error was from running command '/opt/cellranger-7.1.0/lib/bin/STAR'
Command '['/opt/cellranger-7.1.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', 'gex_reference/star', '--runThreadN', '1', '--genomeFastaFiles', 'gex_reference/fasta/genome.fa', '--sjdbGTFfile', 'gex_reference/genes/genes.gtf', '--limitGenomeGenerateRAM', '17179869184', '--genomeSAsparseD', '1', '--genomeSAindexNbases', '12', '--genomeChrBinNbits', '18']' died with <Signals.SIGKILL: 9>.
Check stdout and stderr for more information.
Work dir:
/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/84675ddc3e7ec8e1d28028cce4219541/work/7a/71cd10215614ad213e645e89fdfa2e
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/84675ddc3e7ec8e1d28028cce4219541/meta/nextflow.log' file for details
Nextflow stderr:
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