pditommaso
commented
2 months ago This is not a nextflow issue report.
Closed jiwonhong95 closed 2 months ago
pditommaso
commented
2 months ago This is not a nextflow issue report.
jiwonhong95
commented
2 months ago Hi Paolo,
could you be more specific in where I could report this issue then?
-----Original Message-----
From: "Paolo Di @.>
To: @.>;
Cc: @.>; @.>;
Sent: 2024. 8. 16. (금) 19:03 (GMT+09:00)
Subject: Re: [nextflow-io/nextflow] Process NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) terminated with an error exit status (1) ERROR (Issue #5231)
This is not a nextflow issue report. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
pditommaso
commented
2 months ago Main problem this looks like a pipeline error, not a Nextflow issue. You may want to consider to report to https://github.com/nf-core/rnaseq repository
Bug report
(Please follow this template replacing the text between parentheses with the requested information)
Expected behavior and actual behavior
nexflow runs without error
Steps to reproduce the problem
nextflow run \ nf-core/rnaseq \ --input ../samplesheet_snu_rna_test.csv \ --outdir ./ \ --gtf ../Homo_sapiens.GRCh38.100.gtf \ --fasta ../Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa \ --igenomes_ignore \ --genome null \ -profile docker
to run nexflow nraseq pipeline.
Program output
(env_nf) proteomics@ubuntu:/data/nextflow/RNA_seq_test/20240816$ nextflow run \
N E X T F L O W ~ version 24.04.4
Launching
https://github.com/nf-core/rnaseq[intergalactic_goldstine] DSL2 - revision: b89fac3265 [master]|\ | | /
/ \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--,.,._,' nf-core/rnaseq v3.14.0-gb89fac3Core Nextflow options revision : master runName : intergalactic_goldstine containerEngine : docker launchDir : /data/nextflow/RNA_seq_test/20240816 workDir : /data/nextflow/RNA_seq_test/20240816/work projectDir : /home/proteomics/.nextflow/assets/nf-core/rnaseq userName : proteomics profile : docker configFiles :
Input/output options input : ../samplesheet_snu_rna_test.csv outdir : ./
Reference genome options genome : null fasta : ../Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa gtf : ../Homo_sapiens.GRCh38.100.gtf igenomes_ignore : true
Alignment options min_mapped_reads: 5
!! 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
executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [ 0%] 0 of 1 [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [ 0%] 0 of 1 [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [fd/b477fe] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) [100%] 1 of 1, failed: 1 ✘ executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [ 0%] 0 of 1 [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [fd/b477fe] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) [100%] 1 of 1, failed: 1 ✘ executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [ 0%] 0 of 1 [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [fd/b477fe] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) [100%] 1 of 1, failed: 1 ✘ executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [100%] 1 of 1 ✔ [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [fd/b477fe] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) [100%] 1 of 1, failed: 1 ✘ executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [100%] 1 of 1 ✔ [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [100%] 1 of 1 ✔ [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [fd/b477fe] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) [100%] 1 of 1, failed: 1 ✘ executor > local (31) [7a/6fc897] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [a3/34e54f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [37/d2dc8f] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [4a/5ec51c] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [58/5fe133] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [56/8d310a] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (mysamplename) [100%] 1 of 1 ✔ [61/3724b2] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (mysamplename) [100%] 1 of 1 ✔ [ed/9111ce] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔ [4e/daf529] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (mysamplename) [100%] 1 of 1 ✔ [0e/56ed50] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [a5/2857ad] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (mysamplename) [100%] 1 of 1 ✔ [24/b8eaa8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (mysamplename) [100%] 1 of 1 ✔ [b5/591acc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [e8/b017ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (mysamplename) [100%] 1 of 1 ✔ [77/e0268a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (mysamplename) [100%] 1 of 1 ✔ [61/100e7a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (mysamplename) [100%] 1 of 1 ✔ [10/72fc26] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (mysamplename) [100%] 1 of 1 ✔ [0f/5ca7c2] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE (Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf) [100%] 1 of 1 ✔ [d4/63bc7a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT [100%] 1 of 1 ✔ [d0/c5f98b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (tx2gene.tsv) [100%] 1 of 1 ✔ [c2/ab32b5] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [7a/ad7572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (tx2gene.tsv) [100%] 1 of 1 ✔ [02/4aeb3d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (tx2gene.tsv) [100%] 1 of 1 ✔ [c8/652cd3] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [16/37c8aa] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (mysamplename) [100%] 1 of 1 ✔ [7c/c0cbec] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fa/595250] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (mysamplename) [100%] 1 of 1 ✔ [4b/7f45ce] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0b/89251b] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [fd/b477fe] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename) [100%] 1 of 1, failed: 1 ✘ [b1/240b29] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (mysamplename) [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - -[nf-core/rnaseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename)'
Caused by: Process
NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename)terminated with an error exit status (1)Command executed:
unset DISPLAY mkdir -p tmp export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp qualimap \ --java-mem-size=29491M \ rnaseq \ \ -bam mysamplename.markdup.sorted.bam \ -gtf Homo_sapiens.GRCh38.dna_sm.primary_assembly.filtered.gtf \ -p strand-specific-reverse \ -pe \ -outdir mysamplename
cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ": qualimap: $(echo $(qualimap 2>&1) | sed 's/^.QualiMap v.//; s/Built.$//') END_VERSIONS
Command exit status: 1
Command output: Java memory size is set to 29491M Launching application...
[0.002s][warning][os,thread] Failed to start thread "GC Thread#0" - pthread_create failed (EPERM) for attributes: stacksize: 1024k, guardsize: 4k, detached. [0.003s][error ][gc,task ] Failed to create worker thread
Command error: Java memory size is set to 29491M Launching application...
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=./tmp [0.002s][warning][os,thread] Failed to start thread "GC Thread#0" - pthread_create failed (EPERM) for attributes: stacksize: 1024k, guardsize: 4k, detached. [0.003s][error ][gc,task ] Failed to create worker thread
Work dir: /data/nextflow/RNA_seq_test/20240816/work/fd/b477fe23785ce932e707fb957bdbe3
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
Environment
$SHELL --version) version 4.3.48(1)-release (x86_64-pc-linux-gnu)Additional context
Hello, new to nextflow and thank you for a great tool! I tried using it in my linux server and I cant get rid of this Process
NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (mysamplename)terminated with an error exit status (1) error that keeps occuring. Tried to upgrade as well as downgrade docker and edited the config file so that more memory is given for QUALIMAP_RNASEQ step, yet not much success. I replaced the original specific sample name with "mysamplename" to post online.Attached is the log from the work directory mentioned and the .nextflow.log
.command.log .nextflow.log
Any suggestions on how to fix this? Thank you in advance!