ARM Megatests #336
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Apr 11, 2025 in 0s
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Check failure on line 1 in Test pipeline by skipping trimming options
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Test pipeline by skipping trimming options.Params: --skip_trimming
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1 of 2 assertions failed
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Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [berserk_perlman] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]
WARN: Invalid config manifest attribute `contributors`
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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: The operator `first` is useless when applied to a value channel which returns a single value by definition
[d8/5d94e7] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[d3/df40d5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[41/338306] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[ee/bf72db] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[75/b4cfe2] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[24/4779d0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[6d/f8afc3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[4d/a79bbd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[4f/eb6273] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[02/1d55bd] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[38/2217e7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[18/66f538] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[91/2e526c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[86/11bced] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[35/1d53de] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[d3/572c77] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[5e/317aff] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[f3/c380c1] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[94/b4798b] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[48/53c7b5] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[92/b39173] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[3f/f8745c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[0f/1ee398] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[04/a7629d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[91/cf9ecb] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[6b/0237e2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[6c/23e8bf] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP2)
[0d/4928ad] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP1)
[e0/aa74d7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP2)
[77/9273d0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP1)
[41/d657dd] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[05/62c648] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)
[67/7250e8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[2c/77a424] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP2)
[36/d3cc04] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[01/4fcdee] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP1)
[6e/e24a65] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[1e/d36ee5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_IAA_30M_REP1)
[08/41f046] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[ee/72395e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[d5/33bbfe] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[32/a4e454] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[ab/ca12f5] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[16/745371] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[0f/3dff09] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)
[ba/e74ec2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[92/d58a88] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)
[d1/07f421] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[43/0bece7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[28/20b71b] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[db/4bb5b7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[27/24da7f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[37/a68b72] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP2)
[97/59da57] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[fa/ecf493] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[08/4f98c6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[ab/7a515f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[7c/c4d987] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[57/ad8fd5] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[f3/a955f9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[d6/c8e5bf] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[f6/34da45] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[f9/266335] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[ce/11fd52] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[ec/da745e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[93/9b1253] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[8a/972dc7] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[1c/b0ea03] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[5c/8ef877] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[48/bf232d] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[e5/bcd0f3] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[f9/633376] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[71/f9a4f3] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[3b/68c7f1] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP1)
[97/d141ca] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[0d/d1a332] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[a4/0eba89] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[ea/056f0e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[c8/c1a8e6] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[0d/94b522] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[bc/e6f350] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[b3/4bca6d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[1e/7401b7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[cb/856c5c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[db/77b3d1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[02/8494d6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[f3/35bde8] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[f1/bf7475] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[20/05b8cb] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[41/6bd051] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[b8/6bbc6b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[6a/51ac01] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[a8/897fb6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[aa/9a8a30] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[0e/65c0a8] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[9e/fe77fd] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[2d/b89ec6] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[fc/4124ef] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[09/7da5f6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[23/238f52] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[c7/349108] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[5b/4376fc] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[e3/e9ba89] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[b2/12630b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[39/f12387] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[58/2f831a] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[6d/ba3b40] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null)
[dd/fb1dee] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[f3/96ac60] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[8f/5e1914] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[b0/8aa6f5] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[70/c77941] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[7e/f5566a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[56/46d178] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[91/50155b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[2e/5170fd] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[b4/d9bb30] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[fa/554289] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[74/05c709] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[ed/83e2f6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[2c/e5b2ed] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[b4/900de8] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[e5/4d99e7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[b0/75766d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[a6/9cd8f7] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[cc/655e17] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[65/85f624] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[81/2a6ccd] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[0a/7f48f8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[98/0467f7] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[71/2e9845] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[31/948b93] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[5d/b40930] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[a3/63c0f9] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[46/b0a451] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[91/04e0e1] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[88/f8d782] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[46/3cc773] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[fa/ca2b89] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[df/453133] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[9e/76c8fc] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[7f/290a8a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[4c/e85224] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[ff/ab154c] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[48/daf343] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[eb/867ac7] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[3d/1b3d4b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[68/74853c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[f0/2e3c75] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[d8/2e9b30] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[d2/0e3100] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[81/43a052] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[5f/9f0b59] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[1a/44fabf] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[2a/bc682b] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[91/f45ed0] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
[9e/f3517b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[a9/efddae] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[aa/3ae824] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[f5/a4d21d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[e9/fd7fe1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[2c/1a7f70] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[78/e7afb2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[d4/8bf243] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[5b/d40b76] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[2d/405f1b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[48/62ae45] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[43/18c64b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[3f/f6732c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[3a/70a820] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[94/c6d2d2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[00/fb8fc9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[a6/2d8b7d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[e9/8923b1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[47/ea0821] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[9a/becc0b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[5f/0973be] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[fd/8b2ce8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[e6/303b34] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[60/ee273c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[bc/e5c6d1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[72/7984cc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[fb/55383a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[c0/0054f8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[bb/2bdd1e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[48/dad50d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[ab/fcdd78] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[83/440717] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[f8/32604c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[e6/be7359] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[b7/a6ab3f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[97/4b7ced] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[0d/2fdc88] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[c3/28d987] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[71/3d9b80] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[8e/2afd68] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
[1c/304c80] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples)
[f0/2459c9] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples)
[04/c184b4] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples)
[e2/9a36ca] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)
[01/e2c145] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD: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`
[0e/77f80e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[c0/e0b6ea] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[0;35m[nf-core/rnaseq][0;32m Pipeline completed successfully [0m-
Nextflow stderr:
Nextflow 24.10.5 is available - Please consider updating your version to it
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