ARM Megatests #336
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Apr 11, 2025 in 0s
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Check failure on line 1 in Test pipeline with STAR aligner and RSEM for quantification
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Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 25.02.3-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [small_spence] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]
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[0;34mconfigFiles : [0;32m/home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/tests/nextflow.config[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* 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: The following invalid input values have been detected:
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both '--gtf' and '--gff' parameters have been provided.
Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When using '--additional_fasta <FASTA_FILE>' the aligner index will not
be re-built with the transgenes incorporated by default since you have
already provided an index via '--rsem_index <INDEX>'.
Set '--additional_fasta <FASTA_FILE> --rsem_index false --gene_bed false --save_reference'
to re-build the index with transgenes included and the index and gene BED file will be saved in
'results/genome/index/rsem/' for re-use with '--rsem_index'.
Ignore this warning if you know that the index already contains transgenes.
Please see:
https://github.com/nf-core/rnaseq/issues/556
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[1a/ba3e49] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[68/fdf44d] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[54/0eb936] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[10/a9250a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[11/ceae8d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[47/e9b308] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[06/e374e1] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[1a/4f355d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[ea/1116ac] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_RSEM_INDEX (rsem.tar.gz)
[47/6e5ab3] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[f3/5e1954] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[ff/ec340b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[a5/b8132a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[f5/94c11f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[27/f2b593] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[27/8c0889] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[f5/250d60] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[ce/d498f6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[98/952c30] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[a5/a63dc7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[28/b01047] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[fd/162bd9] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP1)
[c6/344380] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP2)
[0d/d20f9d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_IAA_30M_REP1)
[86/85d1eb] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[b1/8eb4c4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[da/0bebbf] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP2)
[72/ea275a] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[40/48cceb] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[eb/6a78cc] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[55/7d6c75] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP1)
[cb/4e7905] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[13/a04721] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[a4/256e37] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[b4/00022f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[be/764823] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[5f/ee90cc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP1)
[e5/c6ec19] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_IAA_30M_REP1)
[21/10f03d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP2)
[d5/ba9fb2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP2)
[24/35e5fa] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (RAP1_UNINDUCED_REP1)
[e0/c42734] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[12/75308c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (RAP1_IAA_30M_REP1)
[27/6689bd] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[80/3981f2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (WT_REP2)
[55/db0e86] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[2e/95c0b0] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (RAP1_UNINDUCED_REP2)
[07/ad52c6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[76/3251ba] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP1)
[9f/0d2405] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[5d/a70114] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[5c/074eee] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[d7/b1c5af] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[f7/0b6954] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[4e/7706a9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[01/9b2975] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[a0/85fd6a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[a1/3066ab] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[50/0913e2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[3e/1c1bfe] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[77/9281b8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[b9/97fb8c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[cc/b95235] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[d0/ae434c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[80/806825] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[4c/e89137] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[42/28002c] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[a9/fe53aa] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[4b/d5460e] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[fc/df6b42] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[9f/a2a5eb] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[12/050498] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[b6/eb97fd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[3b/16261e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[10/385c03] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[41/f981c1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[e3/181861] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[a5/9cfd3c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[73/014335] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (WT_REP1)
[e3/40a845] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[46/6ec211] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[28/4dc434] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[70/0f957b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[db/cbd816] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[9a/db6d62] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[70/d50aa8] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[b9/956f4a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[f8/048e58] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[d3/ee1b8e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[b9/0de3c0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[82/22a9c2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[bc/7eeb73] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[a7/e3e0d6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[e6/2512c0] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[1e/f37913] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[70/50d048] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[4b/6c6ed3] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[65/d1fd6e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[d5/1f020e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[73/96cd70] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[83/cb0728] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[07/432d73] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[72/cd78bb] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[24/d2de48] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[27/081ffd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[02/b805a2] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[d4/d0139f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[42/a1ccad] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[42/be119a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[91/faaa44] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[62/bdce21] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[28/59df59] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[52/bf9f69] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[e4/577aa5] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[d9/303e56] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[d2/1c08df] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[b1/f0133d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[6c/575a06] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[9e/402faf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[6f/0e6deb] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[65/1056cb] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[64/5f9fc9] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[b2/c6acb7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[fd/279fd6] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[65/76761e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[f4/9cab62] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[f9/d0ea00] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[20/ef27a6] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[fe/2599d3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[d2/8c1914] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[aa/91d0ce] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[8a/86375f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[df/c977ca] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[0f/979d4b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[a6/f1cb4f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[06/e3fbf1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[e7/e7991a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[7c/aa31c6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[fd/1ea727] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[36/1dcd93] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[3a/8a0b0e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_MERGE_COUNTS
[d7/9e218e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[62/3edd53] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[d9/1bd085] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[77/e98f6b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[61/4adc0e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[03/cda497] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[1d/167c36] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_RSEM
[f7/718ca2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[c0/1fc6d6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[d6/a3e443] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[01/316ad4] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[b1/6242a0] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[7b/2d8d18] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[7f/635efc] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[91/e8f36a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[44/3f71e2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[de/e017eb] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[83/88f982] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[f8/f5f732] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[b4/6efd3e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[1b/f3ddc2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[3a/016469] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[68/88853a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[10/fec06e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[5d/201a87] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[d2/843828] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[e0/06f701] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[c6/26c957] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[c1/42b57d] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[84/359518] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[69/6ae04a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[fd/432be6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[01/bb5535] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[e1/df33cf] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[06/594bce] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[ef/1b9fae] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[0d/6d6191] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[b1/04843c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[4c/6e063d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[25/2bce51] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[6f/2de6d1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[c3/e2c01f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[6b/457594] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[a2/c5714e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[78/7052eb] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[78/80d429] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[95/fc2345] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[f9/9546c6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[20/4043b6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[6c/46f72d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[cd/ae3f4b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[db/280e1a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[0b/fdf536] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[6a/889c4a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[22/6455ba] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[5f/b839f9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[e0/552535] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[8b/ca4829] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[e2/245cd4] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[3b/c4e2e1] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
WARN: Access to undefined parameter `enable_multiqc_ai` -- Initialise it to a default value eg. `params.enable_multiqc_ai = some_value`
[be/be356c] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
[ad/fc4cab] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
-[0;35m[nf-core/rnaseq][0;32m Pipeline completed successfully [0m-
Nextflow stderr:
Check failure on line 1 in Test pipeline with STAR aligner and RSEM for quantification
github-actions / JUnit Test Report
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem - stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 25.02.3-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [big_pike] DSL2 - revision: 85c9b75b8b
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq 3.19.0dev[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv[0m
[0;34moutdir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/f0d7229c27866570775b014cf52983b8/output[0m
[1mReference genome options[0m
[0;34mfasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta[0m
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[0;34mgff : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz[0m
[0;34mtranscript_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta[0m
[0;34madditional_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz[0m
[0;34mhisat2_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz[0m
[0;34mrsem_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz[0m
[0;34msalmon_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz[0m
[0;34mhisat2_build_memory : [0;32m3.GB[0m
[1mRead filtering options[0m
[0;34mbbsplit_fasta_list : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt[0m
[1mUMI options[0m
[0;34mumitools_bc_pattern : [0;32mNNNN[0m
[1mAlignment options[0m
[0;34maligner : [0;32mstar_rsem[0m
[0;34mpseudo_aligner : [0;32msalmon[0m
[1mProcess skipping options[0m
[0;34mskip_bbsplit : [0;32mfalse[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description : [0;32mMinimal test dataset to check pipeline function[0m
[1mGeneric options[0m
[0;34mpipelines_testdata_base_path : [0;32ms3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/[0m
[0;34mtrace_report_suffix : [0;32m2025-04-11_20-03-20[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32mbig_pike[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mcontainer.BBMAP_BBSPLIT : [0;32mcommunity.wave.seqera.io/library/bbmap:39.10--168578230ff6490a[0m
[0;34mcontainer.BEDTOOLS_GENOMECOV : [0;32mcommunity.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4[0m
[0;34mcontainer.BRACKEN_BRACKEN : [0;32mcommunity.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1[0m
[0;34mcontainer.CAT_FASTQ : [0;32mcommunity.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264[0m
[0;34mcontainer.CUSTOM_CATADDITIONALFASTA : [0;32mcommunity.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19[0m
[0;34mcontainer.CUSTOM_GETCHROMSIZES : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.CUSTOM_TX2GENE : [0;32mcommunity.wave.seqera.io/library/python:3.10.4--a643e28963f01eef[0m
[0;34mcontainer.DESEQ2_QC : [0;32mcommunity.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2[0m
[0;34mcontainer.DUPRADAR : [0;32mcommunity.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612[0m
[0;34mcontainer.FASTP : [0;32mcommunity.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e[0m
[0;34mcontainer.FASTQC : [0;32mcommunity.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29[0m
[0;34mcontainer.FQ_LINT : [0;32mcommunity.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa[0m
[0;34mcontainer.FQ_SUBSAMPLE : [0;32mcommunity.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa[0m
[0;34mcontainer.GFFREAD : [0;32mcommunity.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572[0m
[0;34mcontainer.GTF2BED : [0;32mcommunity.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c[0m
[0;34mcontainer.GTF_FILTER : [0;32mcommunity.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a[0m
[0;34mcontainer.GUNZIP : [0;32mcommunity.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc[0m
[0;34mcontainer.HISAT2_ALIGN : [0;32mcommunity.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60[0m
[0;34mcontainer.HISAT2_BUILD : [0;32mcommunity.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5[0m
[0;34mcontainer.HISAT2_EXTRACTSPLICESITES : [0;32mcommunity.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5[0m
[0;34mcontainer.KALLISTO_INDEX : [0;32mcommunity.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52[0m
[0;34mcontainer.KALLISTO_QUANT : [0;32mcommunity.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52[0m
[0;34mcontainer.KRAKEN2_KRAKEN2 : [0;32mcommunity.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635[0m
[0;34mcontainer.MULTIQC : [0;32mcommunity.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97[0m
[0;34mcontainer.MULTIQC_CUSTOM_BIOTYPE : [0;32mcommunity.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a[0m
[0;34mcontainer.PICARD_MARKDUPLICATES : [0;32mcommunity.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3[0m
[0;34mcontainer.PREPROCESS_TRANSCRIPTS_FASTA_GENCODE : [0;32mcommunity.wave.seqera.io/library/sed:4.7--c9d1b71422302845[0m
[0;34mcontainer.PRESEQ_LCEXTRAP : [0;32mcommunity.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613[0m
[0;34mcontainer.QUALIMAP_RNASEQ : [0;32mcommunity.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a[0m
[0;34mcontainer.RSEM_CALCULATEEXPRESSION : [0;32mcommunity.wave.seqera.io/library/rsem_star:5acb4e8c03239c32[0m
[0;34mcontainer.RSEM_MERGE_COUNTS : [0;32mcommunity.wave.seqera.io/library/sed:4.7--c9d1b71422302845[0m
[0;34mcontainer.RSEM_PREPAREREFERENCE : [0;32mcommunity.wave.seqera.io/library/rsem_star:5acb4e8c03239c32[0m
[0;34mcontainer.RSEQC_BAMSTAT : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_INFEREXPERIMENT : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_INNERDISTANCE : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_JUNCTIONANNOTATION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_JUNCTIONSATURATION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_READDISTRIBUTION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_READDUPLICATION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_TIN : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.SALMON_INDEX : [0;32mcommunity.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423[0m
[0;34mcontainer.SALMON_QUANT : [0;32mcommunity.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423[0m
[0;34mcontainer.SAMTOOLS_FLAGSTAT : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_IDXSTATS : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_INDEX : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_SORT : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_STATS : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SORTMERNA : [0;32mcommunity.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba[0m
[0;34mcontainer.STAR_ALIGN : [0;32mcommunity.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829[0m
[0;34mcontainer.STAR_ALIGN_IGENOMES : [0;32mcommunity.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a[0m
[0;34mcontainer.STAR_GENOMEGENERATE : [0;32mcommunity.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829[0m
[0;34mcontainer.STAR_GENOMEGENERATE_IGENOMES : [0;32mcommunity.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a[0m
[0;34mcontainer.STRINGTIE_STRINGTIE : [0;32mcommunity.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a[0m
[0;34mcontainer.SUBREAD_FEATURECOUNTS : [0;32mcommunity.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e[0m
[0;34mcontainer.SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT: [0;32mcommunity.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065[0m
[0;34mcontainer.TRIMGALORE : [0;32mcommunity.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d[0m
[0;34mcontainer.TXIMETA_TXIMPORT : [0;32mcommunity.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a[0m
[0;34mcontainer.UCSC_BEDCLIP : [0;32mcommunity.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4[0m
[0;34mcontainer.UCSC_BEDGRAPHTOBIGWIG : [0;32mcommunity.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216[0m
[0;34mcontainer.UMICOLLAPSE : [0;32mcommunity.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0[0m
[0;34mcontainer.UMITOOLS_DEDUP : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UMITOOLS_EXTRACT : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UMITOOLS_PREPAREFORRSEM : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UNTAR : [0;32mcommunity.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc[0m
[0;34mlaunchDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/f0d7229c27866570775b014cf52983b8[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/f0d7229c27866570775b014cf52983b8/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/rnaseq/rnaseq[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m/home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/tests/nextflow.config[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* 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: The following invalid input values have been detected:
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both '--gtf' and '--gff' parameters have been provided.
Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When using '--additional_fasta <FASTA_FILE>' the aligner index will not
be re-built with the transgenes incorporated by default since you have
already provided an index via '--rsem_index <INDEX>'.
Set '--additional_fasta <FASTA_FILE> --rsem_index false --gene_bed false --save_reference'
to re-build the index with transgenes included and the index and gene BED file will be saved in
'results/genome/index/rsem/' for re-use with '--rsem_index'.
Ignore this warning if you know that the index already contains transgenes.
Please see:
https://github.com/nf-core/rnaseq/issues/556
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[6a/e27f94] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[8d/7b92e5] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[e8/74b680] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[44/77e6bd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[23/3709ad] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[8d/8403ce] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[09/04f418] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[10/67eef0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[c7/a55ff3] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_RSEM_INDEX (rsem.tar.gz)
[bc/ebdc8a] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[0a/02b5de] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[09/f12134] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[26/fde5ad] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[6d/01289c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[0d/1f4d95] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[d2/52c6bc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[95/ffb1d5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[68/600b3a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[06/8b2967] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Biotype attribute 'gene_biotype' not found in the last column of the GTF file!
Biotype QC will be skipped to circumvent the issue below:
https://github.com/nf-core/rnaseq/issues/460
Amend '--featurecounts_group_type' to change this behaviour.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[4a/f221a7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[63/e9c1ec] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[eb/ac50b9] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[31/3a6aa4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[45/2fb065] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_transcriptome.gtf)
[80/5c9285] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_transcriptome.fasta)
[f8/990a87] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
WARN: Access to undefined parameter `enable_multiqc_ai` -- Initialise it to a default value eg. `params.enable_multiqc_ai = some_value`
[9f/4cb67b] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[0;35m[nf-core/rnaseq][0;33m Pipeline completed successfully with skipped sampl(es)[0m-
-[0;35m[nf-core/rnaseq][0;31m Please check MultiQC report: 5/5 samples skipped since they failed 10000 trimmed read threshold.[0m-
Nextflow stderr:
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