rnaseq
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Published
20 hours ago •
nf-core
nf-core
rsem-calculate-expression fails. 255: sh: bowtie: command not found
Description of the bug
I am trying to run nf-core with RSEM to quantify gene expression. However, the process RSEM calculate expression fails and exits with error code 255. Upon inspection of the working directory (files are in work.zip), bowtie was invoked from rsem-calculate-expression. I do not have bowtie in my PATH and I do not believe this is necessary.
Command used and terminal output
#!/usr/bin/env bash
#$ -cwd
#$ -pe threaded 2
#$ -l mem=8G
#$ -j y
#$ -V
#$ -N nf_rnaseq
# bash command below:
# -with-report execution_report.html\
# -with-timeline execution_timeline.html\
nextflow run\
/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/nf-core-rnaseq-3.8.1\
-resume\
--input samples.csv\
-work-dir ./.work\
--outdir out\
-profile singularity\
[33mNOTE: Nextflow is not tested with Java 1.8.0_302 -- It's recommended the use of version 11 up to 18
(B[m
N E X T F L O W ~ version 22.04.5
Launching `/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/nf-core-rnaseq-3.8.1/main.nf` [tiny_lovelace] DSL2 - revision: 6b989c60f8
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/rnaseq v3.8.1
------------------------------------------------------
Core Nextflow options
runName : tiny_lovelace
containerEngine : singularity
launchDir : /illumina/scratch/deep_learning/jchang6/nfcore-rnaseq
workDir : /illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work
projectDir : /illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/nf-core-rnaseq-3.8.1
userName : jchang6
profile : singularity
configFiles : /illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/nf-core-rnaseq-3.8.1/nextflow.config, /illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/nextflow.config
Input/output options
input : samples.csv
outdir : out
Reference genome options
genome : hg38_encode
fasta : /illumina/scratch/deep_learning/ReferenceGenome/hg38.fa
gtf : /illumina/scratch/deep_learning/ReferenceGenome/genes/GRCh38/gencode.v39/gencode.v39.annotation.gtf
star_index : /illumina/scratch/deep_learning/jchang6/resources/star_rsem_index/
rsem_index : /illumina/scratch/deep_learning/jchang6/resources/star_rsem_index/
gencode : true
save_reference : true
Alignment options
aligner : star_rsem
save_unaligned : true
skip_markduplicates: true
Process skipping options
skip_stringtie : true
skip_deseq2_qc : true
Max job request options
max_cpus : 8
max_memory : 64.GB
max_time : 8.h
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/rnaseq for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
------------------------------------------------------
WARN: =============================================================================
When using '--aligner star_rsem', both the STAR and RSEM indices should
be present in the path specified by '--rsem_index'.
This warning has been generated because you have provided both
'--rsem_index' and '--star_index'. The pipeline will ignore the latter.
Please see:
https://github.com/nf-core/rnaseq/issues/568
===================================================================================
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*
WARN: There's no process matching config selector: .*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_QUANT
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_SE_.*
WARN: There's no process matching config selector: .*:PREPARE_GENOME:RSEM_PREPAREREFERENCE_GENOME
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*
WARN: There's no process matching config selector: .*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_QUANT
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_SE_.*
WARN: There's no process matching config selector: .*:PREPARE_GENOME:RSEM_PREPAREREFERENCE_GENOME
executor > sge (1)
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1
[cb/97faf3] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
WARN: There's no process matching config selector: .*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*
WARN: There's no process matching config selector: .*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_QUANT
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_SE_.*
WARN: There's no process matching config selector: .*:PREPARE_GENOME:RSEM_PREPAREREFERENCE_GENOME
...
executor > sge (22)
[23/22146d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[63/fc35ee] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[f0/f7e81b] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[06/00c214] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[cb/97faf3] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[0b/60d25e] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [100%] 8 of 8 ✔
[b2/afb649] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [ 12%] 1 of 8
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[c6/d4499a] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
executor > sge (22)
[23/22146d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[63/fc35ee] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[f0/f7e81b] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[06/00c214] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[cb/97faf3] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[0b/60d25e] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [100%] 8 of 8 ✔
[b2/afb649] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [ 12%] 1 of 8
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[c6/d4499a] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
executor > sge (22)
[23/22146d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[63/fc35ee] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[f0/f7e81b] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[06/00c214] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[cb/97faf3] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[0b/60d25e] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [100%] 8 of 8 ✔
[b2/afb649] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [ 12%] 1 of 8
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[c6/d4499a] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [ 0%] 0 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (SRR2128819)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (SRR2128819)` terminated with an error exit status (255)
Command executed:
INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
rsem-calculate-expression \
--num-threads 8 \
--temporary-folder ./tmp/ \
\
--paired-end \
\
SRR2128819_1_val_1.fq.gz SRR2128819_2_val_2.fq.gz \
$INDEX \
SRR2128819
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION":
rsem: $(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
Command exit status:
255
Command output:
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S ./star_rsem_index/reference -1 SRR2128819_1_val_1.fq.gz -2 SRR2128819_2_val_2.fq.gz 2> SRR2128819.log | samtools view -b -o ./tmp//SRR2128819.bam -
"bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S ./star_rsem_index/reference -1 SRR2128819_1_val_1.fq.gz -2 SRR2128819_2_val_2.fq.gz 2> SRR2128819.log | samtools view -b -o ./tmp//SRR2128819.bam -" failed! Plase check if you provide correct parameters/options for the pipeline!
Command error:
WARNING: While bind mounting '/illumina/scratch/deep_learning/jchang6:/illumina/scratch/deep_learning/jchang6': destination is already in the mount point list
WARNING: While bind mounting '/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235:/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235': destination is already in the mount point list
[main_samview] fail to read the header from "-".
Work dir:
/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > sge (22)
[23/22146d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[63/fc35ee] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[f0/f7e81b] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[06/00c214] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[cb/97faf3] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[0b/60d25e] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [100%] 8 of 8 ✔
[b2/afb649] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [ 12%] 1 of 8
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[c6/d4499a] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1, failed: 1 ✘
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (SRR2128819)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (SRR2128819)` terminated with an error exit status (255)
Command executed:
INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
rsem-calculate-expression \
--num-threads 8 \
--temporary-folder ./tmp/ \
\
--paired-end \
\
SRR2128819_1_val_1.fq.gz SRR2128819_2_val_2.fq.gz \
$INDEX \
SRR2128819
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION":
rsem: $(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
Command exit status:
255
Command output:
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S ./star_rsem_index/reference -1 SRR2128819_1_val_1.fq.gz -2 SRR2128819_2_val_2.fq.gz 2> SRR2128819.log | samtools view -b -o ./tmp//SRR2128819.bam -
"bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S ./star_rsem_index/reference -1 SRR2128819_1_val_1.fq.gz -2 SRR2128819_2_val_2.fq.gz 2> SRR2128819.log | samtools view -b -o ./tmp//SRR2128819.bam -" failed! Plase check if you provide correct parameters/options for the pipeline!
Command error:
WARNING: While bind mounting '/illumina/scratch/deep_learning/jchang6:/illumina/scratch/deep_learning/jchang6': destination is already in the mount point list
WARNING: While bind mounting '/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235:/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235': destination is already in the mount point list
[main_samview] fail to read the header from "-".
Work dir:
/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
java.nio.channels.ClosedByInterruptException
-[nf-core/rnaseq] Pipeline completed with errors-
WARN: Killing running tasks (7)
A DataflowVariable can only be assigned once. Use bind() to allow for equal values to be passed into already-bound variables.
executor > sge (22)
[23/22146d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[63/fc35ee] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[f0/f7e81b] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[06/00c214] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔
[cb/97faf3] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[0b/60d25e] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [100%] 8 of 8 ✔
[50/d2a6c9] process > NFCORE_RNASEQ:RNASEQ:FASTQC... [100%] 1 of 1
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[c6/d4499a] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1, failed: 1 ✘
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -
[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (SRR2128819)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (SRR2128819)` terminated with an error exit status (255)
Command executed:
INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
rsem-calculate-expression \
--num-threads 8 \
--temporary-folder ./tmp/ \
\
--paired-end \
\
SRR2128819_1_val_1.fq.gz SRR2128819_2_val_2.fq.gz \
$INDEX \
SRR2128819
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION":
rsem: $(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
Command exit status:
255
Command output:
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S ./star_rsem_index/reference -1 SRR2128819_1_val_1.fq.gz -2 SRR2128819_2_val_2.fq.gz 2> SRR2128819.log | samtools view -b -o ./tmp//SRR2128819.bam -
"bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S ./star_rsem_index/reference -1 SRR2128819_1_val_1.fq.gz -2 SRR2128819_2_val_2.fq.gz 2> SRR2128819.log | samtools view -b -o ./tmp//SRR2128819.bam -" failed! Plase check if you provide correct parameters/options for the pipeline!
Command error:
WARNING: While bind mounting '/illumina/scratch/deep_learning/jchang6:/illumina/scratch/deep_learning/jchang6': destination is already in the mount point list
WARNING: While bind mounting '/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235:/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235': destination is already in the mount point list
[main_samview] fail to read the header from "-".
Work dir:
/illumina/scratch/deep_learning/jchang6/nfcore-rnaseq/.work/c6/d4499a8335b21d7fc7b444f8c81235
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
java.nio.channels.ClosedByInterruptException
***** JOB_ID 3203351.1
***** USER jchang6
***** NODE sg-node002
***** QUEUE slice
***** JOB_EXIT_STATUS 1
***** JOB_START_UTC 1659080891
***** JOB_END_UTC 1659081964
***** ELAPSED_TIME_S 1073.24
***** EXCLUSIVE_JOB NO
***** CPU_USED_S 94.77
***** CPU_CORES_AVAIL 4
***** CPU_USE_PCT 2.21
***** MEM_LIMIT_G 8.00
***** MEM_USED_G 1.01
***** MEM_USE_PCT 12.62
***** INFO Low CPU utilisation, consider lower number of CPU threads
***** INFO Low memory utilisation, consider reducing mem request
***** END
Relevant files
System information
nextflow version 22.04.5.5708 Hardware: HPC Executor: sge Container: singularity OS: CentOS 7 Version of nf-core/rnaseq: 3.8.1
