ARM Megatests #336
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Apr 11, 2025 in 0s
2 tests run, 0 passed, 0 skipped, 2 failed.
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Check failure on line 1 in Test pipeline without a group type for featureCounts
github-actions / JUnit Test Report
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [elated_franklin] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]
WARN: Invalid config manifest attribute `contributors`
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[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
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[0;32m`._,._,'[0m
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[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/4eebe4fc681b15c3d259418d91762bd5[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/4eebe4fc681b15c3d259418d91762bd5/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: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
[2b/f77309] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[86/c3919d] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[2f/753a7c] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[0f/50b956] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[de/13cebd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[d1/32c574] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[fe/93b9d0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[1d/990554] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[fb/8e46d4] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[9e/9adf58] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[c9/913a19] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[8b/d5136a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[05/dde695] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[46/edaa23] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[c2/5c87ac] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[db/fc5870] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[7a/2304d5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[29/4baf92] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[87/87595c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP1)
[a8/771d66] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_IAA_30M_REP1)
[38/db32a4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[9e/b865a9] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[e9/60d9de] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[27/0ffa7c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[8d/d33ccf] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP2)
[e1/1765a9] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[86/13c893] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[98/e70051] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[2c/b68eda] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[5d/706cbc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP2)
[5d/79e871] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP1)
[1c/8fa5ef] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[c1/180ddc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[23/6b2a0d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[74/a41165] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[15/aca16a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[20/5cbe58] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP2)
[a2/6fdc51] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_IAA_30M_REP1)
[6a/a26996] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP1)
[9d/3466e6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP2)
[19/5325d8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[b7/aaa92e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)
[4d/48df40] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[89/735d8f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)
[62/17c6e7] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[b7/9053b3] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP1)
[2c/046854] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP2)
[46/15f9cf] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[a4/56c400] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[6b/979202] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[96/496200] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP1)
[ee/fcd044] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[f1/201eaa] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[bf/095c7b] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[a9/4ee6c2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[e4/058475] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[42/50489b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[bd/0e251f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[86/cbaeb9] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[89/fe55b7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[1e/a28e22] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[e9/f29c78] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[15/d98711] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[bf/f2137a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP2)
[78/ac13da] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[fb/2782e4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[dc/50e3ef] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[7e/347788] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[a9/7e3f71] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[8a/10fbba] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[32/20ce6b] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[d1/8b3444] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[33/c3c580] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[6f/1d4dd1] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[c4/01440a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[f8/eb123b] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[79/0cc81e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[06/a830e5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[50/731ddd] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[81/0c0ddf] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)
[35/2660c1] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[aa/05fab5] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[a9/82acce] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[68/9d7860] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[83/efc858] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[3b/a0965f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[0a/3945c0] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[95/9de176] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[c4/5c7905] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[8c/29e871] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[46/1650cf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[fa/ac01e0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[ff/1f4c51] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[63/1a17c2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[9b/123bfa] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[90/4b31cc] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[0d/e94aa3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[76/8fb80a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[0f/de6696] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[28/f8e3e5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[cd/894394] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[bd/41e8af] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[15/e2fa73] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[f0/59cdf0] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[36/e225a3] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[23/a8c800] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[aa/80c257] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[b4/c81d09] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[10/c2c973] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[65/c10e35] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[b1/11fed5] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[e5/11ada0] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[4c/395846] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[5a/543740] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[86/1a3073] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[d7/d3472d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[37/09b2dd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[5a/8007c2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[ed/bd70de] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[51/994cb1] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[c6/1b2871] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[12/f252d4] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[17/418bb6] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[1a/56aebc] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[21/c3ce85] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[cb/1d5d6e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[2a/eb9995] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[77/34a223] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[88/83a821] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[b8/f3b636] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[e8/75e961] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[eb/8166d9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[92/6ea60a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[2a/c406be] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[21/af298d] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[b5/6f0bb7] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[2a/60aabe] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP1)
[fb/333942] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[fc/64d29e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[ee/32adbc] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[17/d7a6f2] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[51/ceaa6e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[b5/eb1186] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[35/76e05a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null)
[89/92fd79] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[51/4c790c] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[19/b9b886] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[c1/904c8b] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[48/ff7f78] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[5b/2e69a1] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[5e/8e9aaf] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[c0/86c30e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[91/84d836] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[ce/754639] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[39/43aec4] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[b7/6da468] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[e3/56766e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[9a/8e0d1d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[36/ebebb7] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[a3/581135] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[5d/9388a8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[79/274bd2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[7b/22aff1] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[bf/10883a] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[2d/fa180d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[88/02d415] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
[42/954079] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[24/9070f7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[23/7bfc4e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[65/252cfd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[4d/e2bc8f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[4e/330997] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[e5/69e661] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[11/db533e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[9b/b13548] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[f0/31f292] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[8b/f99732] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[35/e77141] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[8f/4de680] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[ca/59f192] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[da/ebaaff] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[4f/e13295] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[04/4642bf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[c0/89d614] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[25/1a4e77] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[ad/12a879] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[93/a37307] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[19/c5ffdc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[5a/e11e6d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[1e/9cede5] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[dd/9b65f4] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[09/359f72] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[ab/a3df50] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[8c/9bc397] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[ad/1e770e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[07/5f426a] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
[e2/02ae84] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples)
[08/dd4c7a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples)
[ad/8f6934] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)
[1e/50827c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples)
[00/e63d8d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[4a/ec733a] 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`
[c7/a28aef] 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
Check failure on line 1 in Test pipeline without a group type for featureCounts
github-actions / JUnit Test Report
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false - stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [trusting_hawking] DSL2 - revision: 85c9b75b8b
WARN: Invalid config manifest attribute `contributors`
-[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
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[0;34moutdir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/7ed288f7b5d8093a4d80900f4076c3d1/output[0m
[1mReference genome options[0m
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[0;34mhisat2_build_memory : [0;32m3.GB[0m
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[1mRead filtering options[0m
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[1mUMI options[0m
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[1mAlignment options[0m
[0;34mpseudo_aligner : [0;32msalmon[0m
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[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_20-03-39[0m
[1mCore Nextflow options[0m
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[0;34mcontainerEngine : [0;32mdocker[0m
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[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/7ed288f7b5d8093a4d80900f4076c3d1[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/7ed288f7b5d8093a4d80900f4076c3d1/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: The operator `first` is useless when applied to a value channel which returns a single value by definition
[0b/16d843] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[31/e1e039] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[17/44fbb8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[96/51f497] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[bd/8f7eb9] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[fe/0a384d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[e0/2b2039] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[b0/99b1f5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[56/621cd0] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[b5/ceee91] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[eb/925ff2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[fa/81764d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[18/a1d4aa] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[7e/89c63e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[7e/d3ce7d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[17/2aa5de] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[ca/a1508b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[bd/e59174] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[5b/a44db2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[47/bd1a4c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[85/8cf082] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[e9/7b3850] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[af/59fbc4] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_transcriptome.fasta)
[9e/e4c4b8] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_transcriptome.fasta)
[ba/d88fd1] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_transcriptome.gtf)
[23/9c6d54] 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`
[44/f2c70a] 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:
Nextflow 24.10.5 is available - Please consider updating your version to it
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