You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am running nf-core/rnaseq with the following command:
nextflow run nf-core/rnaseq
-r 3.14.0
-profile docker
--input /media/unidad/Expansion/Raw_Data/RNAseq_MS/samplesheet.csv
--outdir /media/unidad/Expansion/analysis_MS_nfcore/results/rnaseq
--fasta /media/unidad/Expansion/analysis_MS_nfcore/database/genomes/GRCh38/genome.fasta
--gtf /media/unidad/Expansion/analysis_MS_nfcore/database/genomes/GRCh38/genes.gtf
--transcript_fasta /media/unidad/Expansion/analysis_MS_nfcore/database/genomes/GRCh38/transcript.fasta
--star_index /media/unidad/Expansion/analysis_MS_nfcore/database/indexes/GRCh38/STAR
--salmon_index /media/unidad/Expansion/analysis_MS_nfcore/database/indexes/GRCh38/SALMON --aligner star_salmon -w /mnt/MyBook/work
--max_cpus 6
--max_memory 50.GB
--save_unaligned
-resume`
and I obtained the following error:
`-[nf-core/rnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (HCMS01)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (HCMS01)` terminated with an error exit status (1)
Command executed:
junction_saturation.py \
-i HCMS01.markdup.sorted.bam \
-r genes.bed \
-o HCMS01 \
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION":
rseqc: $(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Unable to find image 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' locally
5.0.3--py39hf95cd2a_0: Pulling from biocontainers/rseqc
642efca944a0: Already exists
bd9ddc54bea9: Already exists
4778d18b334d: Pulling fs layer
4778d18b334d: Download complete
4778d18b334d: Pull complete
Digest: sha256:9fc7027efc23a9dd2309ead1d285034da324eae64e6e940cb0760f4525fa28aa
Status: Downloaded newer image for quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[E::idx_find_and_load] Could not retrieve index file for 'HCMS01.markdup.sorted.bam'
reading reference bed file: genes.bed ... Invalid bed line (skipped): 1 0 248956422 chromosome:1 . . GRCh38 chromosome . ID=chromosome:1;Alias=CM000663.2,chr1,NC_000001.11
Traceback (most recent call last):
File "/usr/local/bin/junction_saturation.py", line 97, in <module>
main()
File "/usr/local/bin/junction_saturation.py", line 83, in main
obj.saturation_junction(outfile=options.output_prefix, refgene=options.refgene_bed, sample_start=options.percentile_low_bound,sample_end=options.percentile_up_bound,sample_step=options.percentile_step,min_intron=options.minimum_intron_size,recur=options.minimum_splice_read, q_cut = options.map_qual)
File "/usr/local/lib/python3.9/site-packages/qcmodule/SAM.py", line 3928, in saturation_junction
exon_starts = list(map( int, fields[11].rstrip( ',\n' ).split( ',' ) ))
ValueError: invalid literal for int() with base 10: '0.79;logic_name=cpg'
Work dir:
/mnt/MyBook/work/66/dcc3242a95a1e8cabbb89d3b6c34cf
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Description of the bug
I am running nf-core/rnaseq with the following command:
the gtf file was obtained from ENSEMBL:
and the gene.bed file was created from the gtf file using GTF2BED:
}
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: