/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-03-26--14-55-12/scripts/Transcriptomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3624_2026-03-26--14-55-18_o.log -------------------------------------------------- Job runs on fgcz-c-095 at /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923 sample 1 S1_undiff 2 S2_undiff 3 S3_undiff 4 S4_diff 5 S5_diff 6 S6_diff fastq_1 1 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S1a_undiff_R1-subsample.fastq.gz 2 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S2_undiff_R1-subsample.fastq.gz 3 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S3_undiff_R1-subsample.fastq.gz 4 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S4_diff_R1-subsample.fastq.gz 5 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S5_diff_R1-subsample.fastq.gz 6 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S6_diff_R1-subsample.fastq.gz strandedness 1 auto 2 auto 3 auto 4 auto 5 auto 6 auto N E X T F L O W ~ version 25.10.4 Launching `https://github.com/nf-core/rnaseq` [golden_easley] DSL2 - revision: 13328f7391 [3.23.0] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/rnaseq 3.23.0 ------------------------------------------------------ Input/output options input : samplesheet.csv outdir : _result Reference genome options fasta : /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa gtf : /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.gtf UMI options umi_discard_read : 0 umitools_grouping_method : unique Alignment options salmon_quant_libtype : A Quality Control contaminant_screening : kraken2 kraken_db : /srv/GT/databases/kraken2/Standard/ bracken_precision : D Generic options trace_report_suffix : 2026-03-26_14-55-28 Core Nextflow options revision : 3.23.0 runName : golden_easley containerEngine : singularity container..*STAR_ALIGN_IGENOMES : community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc container.STAR_GENOMEGENERATE_IGENOMES : community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc container..*PARABRICKS_STARGENOMEGENERATE: community.wave.seqera.io/library/htslib_samtools_star_gawk:4de2f983041d42e6 launchDir : /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923 workDir : /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923/work projectDir : /home/trxcopy/.nextflow/assets/nf-core/rnaseq userName : trxcopy profile : singularity configFiles : /home/trxcopy/.nextflow/assets/nf-core/rnaseq/nextflow.config, /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923/custom_resources.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * 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 [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT - [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT - [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT - [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 6 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT - [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 20 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT - [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 30 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER - [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX - [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT - [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition [- ] NFC…:PREPARE_GENOME:GTF_FILTER | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [- ] NFC…ER_SETSTRANDEDNESS:FQ_LINT | 0 of 6 [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (8) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [68/eca3cf] NFC…NDEDNESS:FQ_LINT (S5_diff) | 0 of 6 [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (8) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [68/eca3cf] NFC…NDEDNESS:FQ_LINT (S5_diff) | 0 of 6 [- ] NFC…UMITOOLS_TRIMGALORE:FASTQC - [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE - [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (14) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [fa/eb2b66] NFC…MGALORE:FASTQC (S1_undiff) | 0 of 6 [- ] NFC…OOLS_TRIMGALORE:TRIMGALORE | 0 of 6 [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (15) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 0 of 6 [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (15) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 0 of 6 [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING - [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (16) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 1 of 6 [- ] NFC…ESS:FQ_LINT_AFTER_TRIMMING | 0 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (17) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 1 of 6 [fd/c3098c] NFC…T_AFTER_TRIMMING (S5_diff) | 0 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE - [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (17) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 1 of 6 [fd/c3098c] NFC…T_AFTER_TRIMMING (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE | 0 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (18) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 1 of 6 [fd/c3098c] NFC…T_AFTER_TRIMMING (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 0 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (18) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [b2/391edc] NFC…ALORE:TRIMGALORE (S5_diff) | 1 of 6 [fd/c3098c] NFC…T_AFTER_TRIMMING (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (19) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [fd/c3098c] NFC…T_AFTER_TRIMMING (S5_diff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (19) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [fd/c3098c] NFC…T_AFTER_TRIMMING (S5_diff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (20) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (20) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 1 of 1 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (20) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [b6/9d6882] NFC…MON:FQ_SUBSAMPLE (S5_diff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (21) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (21) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 1 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (21) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ae/a5ff29] NFC…ORE:TRIMGALORE (S2_undiff) | 2 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (22) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (22) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [d8/f7dbe7] NFC…AFTER_TRIMMING (S2_undiff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (23) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (23) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 0 of 1 [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 2 of 2 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (23) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [54/447437] NFC…N:FQ_SUBSAMPLE (S2_undiff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition executor > local (24) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [6a/9252b4] NFC…MON:FQ_SUBSAMPLE (S6_diff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (24) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [6a/9252b4] NFC…MON:FQ_SUBSAMPLE (S6_diff) | 2 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (24) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [9a/4d686f] NFC…ALORE:TRIMGALORE (S6_diff) | 3 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [6a/9252b4] NFC…MON:FQ_SUBSAMPLE (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (25) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e6/37f74f] NFC…ORE:TRIMGALORE (S3_undiff) | 4 of 6 [7f/e201d6] NFC…T_AFTER_TRIMMING (S6_diff) | 3 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [6a/9252b4] NFC…MON:FQ_SUBSAMPLE (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (26) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e6/37f74f] NFC…ORE:TRIMGALORE (S3_undiff) | 4 of 6 [26/a5b903] NFC…AFTER_TRIMMING (S3_undiff) | 3 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [6a/9252b4] NFC…MON:FQ_SUBSAMPLE (S6_diff) | 3 of 3 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (26) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e6/37f74f] NFC…ORE:TRIMGALORE (S3_undiff) | 4 of 6 [26/a5b903] NFC…AFTER_TRIMMING (S3_undiff) | 4 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [6a/9252b4] NFC…MON:FQ_SUBSAMPLE (S6_diff) | 3 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (27) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e6/37f74f] NFC…ORE:TRIMGALORE (S3_undiff) | 4 of 6 [26/a5b903] NFC…AFTER_TRIMMING (S3_undiff) | 4 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [90/39e954] NFC…N:FQ_SUBSAMPLE (S3_undiff) | 3 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (27) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e6/37f74f] NFC…ORE:TRIMGALORE (S3_undiff) | 4 of 6 [26/a5b903] NFC…AFTER_TRIMMING (S3_undiff) | 4 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [90/39e954] NFC…N:FQ_SUBSAMPLE (S3_undiff) | 4 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (29) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ed/d1ec26] NFC…ALORE:TRIMGALORE (S4_diff) | 5 of 6 [f6/1a65f6] NFC…T_AFTER_TRIMMING (S4_diff) | 4 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [90/39e954] NFC…N:FQ_SUBSAMPLE (S3_undiff) | 4 of 4 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (30) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 0 of 1 [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED - [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA - [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES - [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ed/d1ec26] NFC…ALORE:TRIMGALORE (S4_diff) | 5 of 6 [f6/1a65f6] NFC…T_AFTER_TRIMMING (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 4 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (30) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [- ] NFC…SEQ:PREPARE_GENOME:GTF2BED | 0 of 1 [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ed/d1ec26] NFC…ALORE:TRIMGALORE (S4_diff) | 5 of 6 [f6/1a65f6] NFC…T_AFTER_TRIMMING (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 4 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (31) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ed/d1ec26] NFC…ALORE:TRIMGALORE (S4_diff) | 5 of 6 [f6/1a65f6] NFC…T_AFTER_TRIMMING (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 4 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (31) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [ed/d1ec26] NFC…ALORE:TRIMGALORE (S4_diff) | 5 of 6 [f6/1a65f6] NFC…T_AFTER_TRIMMING (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (32) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [f6/1a65f6] NFC…T_AFTER_TRIMMING (S4_diff) | 5 of 6 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (33) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 5 of 6 [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 5 of 5 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (33) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [e3/5a6869] NFC…MON:FQ_SUBSAMPLE (S4_diff) | 5 of 6 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (34) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 5 of 6 [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (34) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 0 of 1 [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (34) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 1 of 1 ✔ [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 0 of 1 [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [- ] NFC…AR_GENOMEGENERATE_IGENOMES | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX - [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (35) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 1 of 1 ✔ [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 1 of 1 ✔ [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [80/5fd03c] NFC…ERATE_IGENOMES (genome.fa) | 0 of 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_INDEX | 0 of 1 [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (36) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 1 of 1 ✔ [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 1 of 1 ✔ [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [80/5fd03c] NFC…ERATE_IGENOMES (genome.fa) | 0 of 1, retries: 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [37/650719] NFC…EX (genome.transcripts.fa) | 0 of 1 [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT - [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… [80/5fd03c] NOTE: Process `NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE_IGENOMES (genome.fa)` terminated with an error exit status (139) -- Execution is retried (1) executor > local (37) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 1 of 1 ✔ [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 1 of 1 ✔ [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [58/24892d] NFC…ERATE_IGENOMES (genome.fa) | 0 of 1, retries: 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [37/650719] NFC…EX (genome.transcripts.fa) | 1 of 1 ✔ [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [- ] NFC…PLE_FQ_SALMON:SALMON_QUANT | 0 of 6 [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… executor > local (38) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 1 of 1 ✔ [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 1 of 1 ✔ [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [58/24892d] NFC…ERATE_IGENOMES (genome.fa) | 0 of 1, retries: 1 [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [37/650719] NFC…EX (genome.transcripts.fa) | 1 of 1 ✔ [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [d5/4cd824] NFC…MON:SALMON_QUANT (S4_diff) | 0 of 6 [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE_IGENOMES (genome.fa)' Caused by: Process `NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE_IGENOMES (genome.fa)` terminated with an error exit status (139) Command executed: samtools faidx genome.fa NUM_BASES=`gawk '{sum = sum + $2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' genome.fa.fai` mkdir star STAR \ --runMode genomeGenerate \ --genomeDir star/ \ --genomeFastaFiles genome.fa \ --sjdbGTFfile genes.filtered.gtf \ --runThreadN 16 \ --genomeSAindexNbases $NUM_BASES \ --limitGenomeGenerateRAM 137338953472 \ Command exit status: 139 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred .command.sh: line 14: 962 Segmentation fault STAR --runMode genomeGenerate --genomeDir star/ --genomeFastaFiles genome.fa --sjdbGTFfile genes.filtered.gtf --runThreadN 16 --genomeSAindexNbases $NUM_BASES --limitGenomeGenerateRAM 137338953472 Work dir: /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923/work/58/24892d07d3cb0f6abd20b57f0d9f5e Container: /misc/fgcz01/nextflow_apptainer_cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-50-50bb64440689d5d7af4bf8ad1032f01aa4e1597e0bb1c82ee91e8cb43943283c-data.img Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for details executor > local (39) [cd/949d78] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ [e8/658f24] NFC…F2BED (genes.filtered.gtf) | 1 of 1 ✔ [b3/b92dae] NFC…PTS_FASTA (rsem/genome.fa) | 1 of 1 ✔ [8c/3ce411] NFC…SAMTOOLS_FAIDX (genome.fa) | 1 of 1 ✔ [58/24892d] NFC…ERATE_IGENOMES (genome.fa) | 0 of 1, retries: 1 ✘ [- ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX - [- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ - [a6/120fbe] NFC…NDEDNESS:FQ_LINT (S4_diff) | 6 of 6 ✔ [2e/cefefa] NFC…RIMGALORE:FASTQC (S6_diff) | 6 of 6 ✔ [e4/c5fc7a] NFC…ORE:TRIMGALORE (S1_undiff) | 6 of 6 ✔ [ff/d1bbca] NFC…AFTER_TRIMMING (S1_undiff) | 6 of 6 ✔ [37/650719] NFC…EX (genome.transcripts.fa) | 1 of 1 ✔ [87/509183] NFC…N:FQ_SUBSAMPLE (S1_undiff) | 6 of 6 ✔ [31/1e03f4] NFC…N:SALMON_QUANT (S2_undiff) | 0 of 6 [- ] NFC…N_STAR:STAR_ALIGN_IGENOMES - [- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX - [- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS - [- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS - Plus 32 more processes waiting for tasks… -[nf-core/rnaseq] Pipeline completed with errors- WARN: Killing running tasks (2) ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE_IGENOMES (genome.fa)' Caused by: Process `NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE_IGENOMES (genome.fa)` terminated with an error exit status (139) Command executed: samtools faidx genome.fa NUM_BASES=`gawk '{sum = sum + $2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' genome.fa.fai` mkdir star STAR \ --runMode genomeGenerate \ --genomeDir star/ \ --genomeFastaFiles genome.fa \ --sjdbGTFfile genes.filtered.gtf \ --runThreadN 16 \ --genomeSAindexNbases $NUM_BASES \ --limitGenomeGenerateRAM 137338953472 \ Command exit status: 139 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred .command.sh: line 14: 962 Segmentation fault STAR --runMode genomeGenerate --genomeDir star/ --genomeFastaFiles genome.fa --sjdbGTFfile genes.filtered.gtf --runThreadN 16 --genomeSAindexNbases $NUM_BASES --limitGenomeGenerateRAM 137338953472 Work dir: /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923/work/58/24892d07d3cb0f6abd20b57f0d9f5e Container: /misc/fgcz01/nextflow_apptainer_cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-50-50bb64440689d5d7af4bf8ad1032f01aa4e1597e0bb1c82ee91e8cb43943283c-data.img Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details WARN: Failed to render execution report -- see the log file for details WARN: Failed to render execution timeline -- see the log file for details ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-03-26--14-55-12/scripts/Transcriptomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3624_2026-03-26--14-55-18_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-03-26--14-55-12/input_dataset.tsv + LAST_JOB=TRUE ++ hostname + echo 'Job runs on fgcz-c-095' + echo 'at /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923' + mkdir /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923 + cd /scratch/NfCoreRnaseq_2026-03-26--14-55-12_temp1448923 + source /usr/local/ngseq/etc/lmod_profile +++ eval 'echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles' ++++ echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ export MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ source /usr/share/lmod/lmod/init/profile +++ '[' -z '' ']' +++ LMOD_ALLOW_ROOT_USE=yes +++ '[' -n '' ']' +++ '[' yes '!=' yes ']' +++ '[' -z /usr/share/modulefiles ']' +++ findExec READLINK_CMD /bin/readlink readlink +++ Nm=READLINK_CMD +++ confPath=/bin/readlink +++ execNm=readlink +++ eval READLINK_CMD=/bin/readlink ++++ READLINK_CMD=/bin/readlink +++ '[' '!' -x /bin/readlink ']' +++ unset Nm confPath execNm +++ findExec PS_CMD /bin/ps ps +++ Nm=PS_CMD +++ confPath=/bin/ps +++ execNm=ps +++ eval PS_CMD=/bin/ps ++++ PS_CMD=/bin/ps +++ '[' '!' -x /bin/ps ']' +++ unset Nm confPath execNm +++ findExec EXPR_CMD /usr/bin/expr expr +++ Nm=EXPR_CMD +++ confPath=/usr/bin/expr +++ execNm=expr +++ eval EXPR_CMD=/usr/bin/expr ++++ EXPR_CMD=/usr/bin/expr +++ '[' '!' -x /usr/bin/expr ']' +++ unset Nm confPath execNm +++ findExec BASENAME_CMD /usr/bin/basename basename +++ Nm=BASENAME_CMD +++ confPath=/usr/bin/basename +++ execNm=basename +++ eval BASENAME_CMD=/usr/bin/basename ++++ BASENAME_CMD=/usr/bin/basename +++ '[' '!' -x /usr/bin/basename ']' +++ unset Nm confPath execNm +++ unset -f findExec +++ '[' -f /proc/1448923/exe ']' ++++ /bin/readlink /proc/1448923/exe +++ my_shell=/usr/bin/bash ++++ /usr/bin/expr /usr/bin/bash : '-*\(.*\)' +++ my_shell=/usr/bin/bash ++++ /usr/bin/basename /usr/bin/bash +++ my_shell=bash +++ case ${my_shell} in +++ '[' -f /usr/share/lmod/lmod/init/bash ']' +++ . /usr/share/lmod/lmod/init/bash ++++ '[' -z '' ']' ++++ case "$-" in ++++ __lmod_vx=x ++++ '[' -n x ']' ++++ set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/share/lmod/lmod/init/bash) Shell debugging restarted ++++ unset __lmod_vx +++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT LMOD_ALLOW_ROOT_USE READLINK_CMD ++ export NGSEQ=/usr/local/ngseq ++ NGSEQ=/usr/local/ngseq ++ export ngsrc=/usr/local/ngseq/srcm ++ ngsrc=/usr/local/ngseq/srcm ++ export ngpkg=/usr/local/ngseq/packages ++ ngpkg=/usr/local/ngseq/packages ++ export ngmdf=/usr/local/ngseq/etc/modules ++ ngmdf=/usr/local/ngseq/etc/modules ++ '[' -d /usr/local/ngseq/. ']' ++ PATH=/usr/local/ngseq/bin:/home/trxcopy/.conda/envs/gi_sushi_jobmanager_2024/bin:/misc/ngseq12/miniforge3/condabin:/usr/local/ngseq/packages/Dev/Ruby/3.3.7/bin:/usr/local/ngseq/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games ++ export PATH ++ LD_LIBRARY_PATH=/usr/local/ngseq/lib:/usr/local/ngseq/lib:/usr/local/ngseq/lib ++ export LD_LIBRARY_PATH ++ alias 'lmodInit=. /usr/local/ngseq/etc/lmod_profile' + export NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + export SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + R --vanilla --slave Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Loading required package: tidyverse ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.1 ✔ stringr 1.6.0 ✔ ggplot2 4.0.1 ✔ tibble 3.3.1 ✔ lubridate 1.9.4 ✔ tidyr 1.3.2 ✔ purrr 1.1.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ lubridate::%within%() masks IRanges::%within%() ✖ dplyr::between() masks data.table::between() ✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse() ✖ dplyr::combine() masks BiocGenerics::combine() ✖ purrr::compact() masks XVector::compact() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first(), data.table::first() ✖ lubridate::hour() masks data.table::hour() ✖ lubridate::isoweek() masks data.table::isoweek() ✖ lubridate::isoyear() masks data.table::isoyear() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ lubridate::mday() masks data.table::mday() ✖ lubridate::minute() masks data.table::minute() ✖ lubridate::month() masks data.table::month() ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position() ✖ lubridate::quarter() masks data.table::quarter() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ lubridate::second() masks S4Vectors::second(), data.table::second() ✖ lubridate::second<-() masks S4Vectors::second<-() ✖ dplyr::slice() masks XVector::slice(), IRanges::slice() ✖ purrr::transpose() masks data.table::transpose() ✖ lubridate::wday() masks data.table::wday() ✖ lubridate::week() masks data.table::week() ✖ lubridate::yday() masks data.table::yday() ✖ lubridate::year() masks data.table::year() ℹ Use the conflicted package () to force all conflicts to become errors Loading required package: logger Added strandedness column: auto Sample sheet written to: samplesheet.csv Sample sheet contents: Custom config written: custom_resources.config // Executor: total available resources for this job executor { name = 'local' cpus = 16 memory = '128.GB' } // Cap all process labels to fit within executor limits process { resourceLimits = [ cpus: 16, memory: '128.GB' ] } Loading module: nextflow/25.10 Loading Nextflow 25.10.4 Using FASTA: /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa Using GTF: /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.gtf Running command: nextflow run nf-core/rnaseq -r 3.23.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.gtf --hisat2_build_memory '200.GB' --gencode 'false' --gffread_transcript_fasta 'false' --gtf_extra_attributes 'gene_name' --gtf_group_features 'gene_id' --featurecounts_group_type 'gene_biotype' --featurecounts_feature_type 'exon' --trimmer 'trimgalore' --min_trimmed_reads '10000' --remove_ribo_rna 'false' --ribo_removal_tool 'sortmerna' --with_umi 'false' --umi_dedup_tool 'umitools' --umitools_extract_method 'string' --umi_discard_read '0' --umitools_grouping_method 'unique' --umitools_dedup_stats 'false' --aligner 'star_salmon' --use_sentieon_star 'false' --use_parabricks_star 'false' --pseudo_aligner_kmer_size '31' --bam_csi_index 'false' --star_ignore_sjdbgtf 'false' --salmon_quant_libtype 'A' --min_mapped_reads '5' --stringtie_ignore_gtf 'false' --kallisto_quant_fraglen '200' --kallisto_quant_fraglen_sd '200' --stranded_threshold '0.8' --unstranded_threshold '0.1' --save_merged_fastq 'false' --save_umi_intermeds 'false' --save_non_ribo_reads 'false' --save_bbsplit_reads 'false' --save_reference 'false' --save_trimmed 'false' --save_align_intermeds 'false' --save_unaligned 'false' --save_kraken_assignments 'false' --save_kraken_unassigned 'false' --extra_fqlint_args '--disable-validator P001' --deseq2_vst 'true' --rseqc_modules 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication' --contaminant_screening 'kraken2' --kraken_db '/srv/GT/databases/kraken2/Standard/' --bracken_precision 'D' --skip_gtf_filter 'false' --skip_gtf_transcript_filter 'false' --skip_bbsplit 'true' --skip_umi_extract 'false' --skip_linting 'false' --skip_trimming 'false' --skip_pseudo_alignment 'false' --skip_markduplicates 'false' --skip_bigwig 'false' --skip_stringtie 'false' --skip_fastqc 'false' --skip_preseq 'true' --skip_dupradar 'false' --skip_qualimap 'false' --skip_rseqc 'false' --skip_biotype_qc 'false' --skip_deseq2_qc 'false' --skip_multiqc 'false' --skip_qc 'false' INFO (ezRun) [2026-03-26 14:55:24] EXECUTED CMD: nextflow run nf-core/rnaseq -r 3.23.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.gtf --hisat2_build_memory '200.GB' --gencode 'false' --gffread_transcript_fasta 'false' --gtf_extra_attributes 'gene_name' --gtf_group_features 'gene_id' --featurecounts_group_type 'gene_biotype' --featurecounts_feature_type 'exon' --trimmer 'trimgalore' --min_trimmed_reads '10000' --remove_ribo_rna 'false' --ribo_removal_tool 'sortmerna' --with_umi 'false' --umi_dedup_tool 'umitools' --umitools_extract_method 'string' --umi_discard_read '0' --umitools_grouping_method 'unique' --umitools_dedup_stats 'false' --aligner 'star_salmon' --use_sentieon_star 'false' --use_parabricks_star 'false' --pseudo_aligner_kmer_size '31' --bam_csi_index 'false' --star_ignore_sjdbgtf 'false' --salmon_quant_libtype 'A' --min_mapped_reads '5' --stringtie_ignore_gtf 'false' --kallisto_quant_fraglen '200' --kallisto_quant_fraglen_sd '200' --stranded_threshold '0.8' --unstranded_threshold '0.1' --save_merged_fastq 'false' --save_umi_intermeds 'false' --save_non_ribo_reads 'false' --save_bbsplit_reads 'false' --save_reference 'false' --save_trimmed 'false' --save_align_intermeds 'false' --save_unaligned 'false' --save_kraken_assignments 'false' --save_kraken_unassigned 'false' --extra_fqlint_args '--disable-validator P001' --deseq2_vst 'true' --rseqc_modules 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication' --contaminant_screening 'kraken2' --kraken_db '/srv/GT/databases/kraken2/Standard/' --bracken_precision 'D' --skip_gtf_filter 'false' --skip_gtf_transcript_filter 'false' --skip_bbsplit 'true' --skip_umi_extract 'false' --skip_linting 'false' --skip_trimming 'false' --skip_pseudo_alignment 'false' --skip_markduplicates 'false' --skip_bigwig 'false' --skip_stringtie 'false' --skip_fastqc 'false' --skip_preseq 'true' --skip_dupradar 'false' --skip_qualimap 'false' --skip_rseqc 'false' --skip_biotype_qc 'false' --skip_deseq2_qc 'false' --skip_multiqc 'false' --skip_qc 'false' Error in ezSystem(cmd) : nextflow run nf-core/rnaseq -r 3.23.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.gtf --hisat2_build_memory '200.GB' --gencode 'false' --gffread_transcript_fasta 'false' --gtf_extra_attributes 'gene_name' --gtf_group_features 'gene_id' --featurecounts_group_type 'gene_biotype' --featurecounts_feature_type 'exon' --trimmer 'trimgalore' --min_trimmed_reads '10000' --remove_ribo_rna 'false' --ribo_removal_tool 'sortmerna' --with_umi 'false' --umi_dedup_tool 'umitools' --umitools_extract_method 'string' --umi_discard_read '0' --umitools_grouping_method 'unique' --umitools_dedup_stats 'false' --aligner 'star_salmon' --use_sentieon_star 'false' --use_parabricks_star 'false' --pseudo_aligner_kmer_size '31' --bam_csi_index 'false' --star_ignore_sjdb Calls: -> ezSystem Execution halted ___STDERR_END___