ERROR ~ Error executing process > 'pipeline:merge_gff_bundles (3)

[Aravind-mss]

Ask away!

I have tried with both fastq , uBMA and BAM inputs but unable make any progress beyond this step. I have used the below way of running the pipeline on my last try. But no luck. The same step failed like before. Please help. nextflow run epi2me-labs/wf-transcriptomes \ --fastq $input \ --de_analysis \ --ref_annotation "$genomedir/GRCh38.p14_genomic.gtf" \ --ref_genome "$genomedir/GRCh38.p14_genomic.fa" \ --sample_sheet "$mydir/samplesheet.csv" \ --out_dir "$mydir/transcriptomics_fastq" -profile singularity

executor > pbspro (110) [46/625c71] validate_sample_sheet | 1 of 1 ✔ [67/de8deb] fastcat (1) | 6 of 6 ✔ [bc/af7649] pip…:preprocess_ref_annotation | 1 of 1 ✔ [e7/1a7ccf] pip…stqIngressResultsInDir (6) | 6 of 6 ✔ [c8/6eda3f] pipeline:getVersions | 1 of 1 ✔ [c0/8add90] pipeline:getParams | 1 of 1 ✔ [eb/ffbc6a] pipeline:preprocess_reads (5) | 6 of 6 ✔ [b9/260bbb] pip…ne:build_minimap_index (1) | 1 of 1 ✔ [2c/ebb78b] pip…nce_assembly:map_reads (6) | 6 of 6 ✔ [15/bf5486] pipeline:split_bam (6) | 6 of 6 ✔ [52/f6a5c4] pip…:assemble_transcripts (58) | 67 of 67 ✔ [cb/b8006b] pipeline:merge_gff_bundles (3) | 1 of 6, failed: 1 [- ] pipeline:run_gffcompare - [- ] pipeline:get_transcriptome - [1a/56fee6] pip…ne:check_annotation_strand | 1 of 1 ✔ [- ] pipeline:merge_transcriptomes - [12/4005f3] pip…ckSampleSheetCondition (1) | 1 of 1 ✔ [- ] pip…inimap_index_transcriptome - [- ] pip…pression:map_transcriptome - [- ] pip…pression:count_transcripts - Plus 6 more processes waiting for tasks… ERROR ~ Error executing process > 'pipeline:merge_gff_bundles (3)'

Caused by: Process pipeline:merge_gff_bundles (3) terminated with an error exit status (1)

Command executed:

echo '##gff-version 2' >> BEL14169A3.gff; echo '#pipeline-nanopore-isoforms: stringtie' >> BEL14169A3.gff;

for fn in BEL14169A3_batch_7.gff BEL14169A3_batch_8.gff BEL14169A3_batch_6.gff BEL14169A3_batch_3.gff BEL14169A3_batch_9.gff BEL14169A3_batch_4.gff BEL14169A3_batch_5.gff BEL14169A3_batch_2.gff BEL14169A3_batch_1.gff; do grep -v '#' $fn >> BEL14169A3.gff

done

workflow-glue summarise_gff BEL14169A3.gff BEL14169A3 transcriptome_summary.pickle

Command exit status: 1 Command output: (empty)

[fabsal74]

I have the same error...

[nrhorner]

Hi @Aravind-mss

Please open another ticket using the bug issue template.

https://github.com/epi2me-labs/wf-transcriptomes/issues/new?assignees=&labels=triage&projects=&template=bug_report.yml