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I'm having some trouble getting the test data to run via singularity with alevin, specifically if I supply my own genome/annotation. It's failing at SIMPLEAF_INDEX
My command was (note specifying 0e5fc8b here to grab the dev branch, given issues #245 , #246, though same error on -r 2.3.2):
nextflow run nf-core/scrnaseq \
-r 0e5fc8b \
-profile test \
-c /jsimonlab/pipelines/nfcore/nextflow.config \
--outdir test \
-work-dir /jsimonlab/scratch/jsimon/nextflow/work \
--fasta GRCh38.primary_assembly.genome.fa \
--gtf gencode.v43.annotation.gtf \
--protocol 10XV2 \
--aligner alevin
My config file here is rather simple and confirmed works for nf-core/rnaseq and nf-core/atacseq:
N E X T F L O W ~ version 23.04.1
[...]
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GRCh38.primary_assembly.genome_genes.gtf)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX (GRCh38.primary_assembly.genome_genes.gtf)` terminated with an error exit status (1)
Command executed:
# export required var
export ALEVIN_FRY_HOME=.
# prep simpleaf
simpleaf set-paths
# run simpleaf index
simpleaf \
index \
--threads 2 \
--fasta GRCh38.primary_assembly.genome.fa \
--gtf GRCh38.primary_assembly.genome_genes.gtf \
--rlen 91 \
-o salmon
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SIMPLEAF_INDEX":
simpleaf: $(simpleaf -V | tr -d '\n' | cut -d ' ' -f 2)
salmon: $(salmon --version | sed -e "s/salmon //g")
END_VERSIONS
Command exit status:
1
Command output:
2023-07-19T13:07:34.313588Z INFO simpleaf::utils::prog_utils: could not find piscem executable, so salmon will be required.
found `salmon` in the PATH at /usr/local/bin/salmon
found `alevin-fry` in the PATH at /usr/local/bin/alevin-fry
found `pyroe` in the PATH at /usr/local/bin/pyroe
2023-07-19T13:07:42.996853Z INFO simpleaf: pyroe cmd : /usr/local/bin/pyroe make-splici GRCh38.primary_assembly.genome.fa GRCh38.primary_assembly.genome_genes.gtf 91 salmon/ref
2023-07-19T13:09:45.799564Z ERROR simpleaf::utils::prog_utils: command unsuccessful (signal: 9 (SIGKILL)): "/usr/local/bin/pyroe" "make-splici" "GRCh38.primary_assembly.genome.fa" "GRCh38.primary_assembly.genome_genes.gtf" "91" "salmon/ref"
Command error:
Error: pyroe failed to return succesfully ExitStatus(unix_wait_status(9))
And I know that the issue is not that the genome/annotation files are corrupt or anything, as the exact same files work fine for nf-core/rnaseq in a full-scale real-world data run
Is this a known issue? Or is there something else I'm missing here?
Also as a side note, specifying all three of --fasta, --gtf, and --transcript_fasta causes a (different) failure at the SIMPLEAF_INDEX step since it accepts either the genome or transcript FASTA but not both. This is not clear from the documentation, at least to me it implies all three are required parameters
error: the argument '--fasta <FASTA>' cannot be used with '--ref-seq <REF_SEQ>'
Command used and terminal output
No response
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered:
Description of the bug
I'm having some trouble getting the
test
data to run viasingularity
withalevin
, specifically if I supply my own genome/annotation. It's failing atSIMPLEAF_INDEX
My command was (note specifying
0e5fc8b
here to grab thedev
branch, given issues #245 , #246, though same error on-r 2.3.2
):My config file here is rather simple and confirmed works for
nf-core/rnaseq
andnf-core/atacseq
:The error produced is:
Which seems a lot like issue #191
However the same exact setup, specifying
--genome hg38
instead of my own files runs successfully:And I know that the issue is not that the genome/annotation files are corrupt or anything, as the exact same files work fine for
nf-core/rnaseq
in a full-scale real-world data runIs this a known issue? Or is there something else I'm missing here?
Also as a side note, specifying all three of
--fasta
,--gtf
, and--transcript_fasta
causes a (different) failure at theSIMPLEAF_INDEX
step since it accepts either the genome or transcript FASTA but not both. This is not clear from the documentation, at least to me it implies all three are required parametersCommand used and terminal output
No response
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: