Nextflow rnaseq finishing early

Nextflow rnaseq finishing early

0

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


RNA-seq


nextflow

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updated 34 minutes ago by

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