Nextflow rnaseq finishing early
Hi I’m running the RNA-seq pipeline from nextflow and I have been running it without problems until this dataset it just stops prematurely saying it has finished when it doesn’t even aligns the reads with salmon. Any ideas what may be going on? I have run the same command
executor > sge (247), local (1)
[98/1b4918] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (genome.fa) [100%] 1 of 1 ✔
[2a/925236] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome.fa) [100%] 1 of 1 ✔
[e4/3f8b75] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) [100%] 1 of 1 ✔
[e1/7cb95a] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[06/36e97e] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) [100%] 1 of 1 ✔
[cd/de51a1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (XLP2_REP9) [100%] 60 of 60 ✔
[6a/4d5cbd] process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (XLP2_REP6) [100%] 60 of 60 ✔
[92/e51954] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (XLP2_REP6) [100%] 60 of 60 ✔
[bb/35c9ca] process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (XLP2_REP6) [100%] 60 of 60 ✔
[be/a86bc8] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN_IGENOMES -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT -
[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE -
[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION -
[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK -
[a5/125832] process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔
[25/d2e429] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [100%] 1 of 1 ✔
-[nf-core/rnaseq] Pipeline completed successfully-
Completed at: 28-Mar-2023 03:00:16
Duration : 4h 42m 16s
CPU hours : 30.1
Succeeded : 248
nextflow run nf-core/rnaseq --input samples.csv --genome GRCh38 --outdir output -r 3.10.1 -resume -profile singularity
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