No Bam and Bai files in the ouput

[KatrinMoller]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.4.0

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

OUTPUT=~/output;
./nextflow run epi2me-labs/wf-transcriptomes
-profile singularity
--bam /merged_output
--de_analysis
--ref_genome /genomes/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
--ref_annotation /genomes/Mus_musculus.GRCm38.98.gtf.gz
--ref_transcriptome Mus_musculus.GRCm38.cdna.all.fa.gz
--sample_sheet /sample_sheets/sample_sheet1.csv
--cdna_kit "SQK-PCS114"
--isoform_table_nrows 10000
--out_dir /analysis/outdir1 -w /analysis/workspace_dir1
--threads 64

Workflow Execution - CLI Execution Profile

singularity

What happened?

The pipeline ran successfully (at least no errors reported), however there are no bam or bai files in the output. I have run this before, with an older version and another dataset, and then I got bam and bai files to view the minimap2 alignments e.g. on IGV. If they are not in the standard output directory, where can I find them?

Relevant log output

Workflow execution completed successfully!

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[etycksen]

I've been adding this to my wf-transcriptomes shell scripts to find and copy the bam files in the work directory to the out directory.

find ./work -type f -name reads_aln_sorted.bam -exec cp '{}' $out_directory ;

[KatrinMoller]

@etycksen thanks for the suggestion. I will try this for sure, also for the .bai files (I'd like to see the coverage and actual isoform reads for some of my transcripts).
I just thought the developers should know, since so far this has been a part of the pipeline and in version 1.4.0 they specifically state:
Changed:

• BAMS are output in to a BAMS directory.

[fgponce]

Apparently it doesn't output these if you use a ref-guided approach but will if you use a precomputed. I was surprised as well since its the first thing I do after running something like this, look at the alignments in igv...having said that i'm now struggling to get past fastcat with a precomputed transcriptome to confirm this...

[KatrinMoller]

@fgponce I actually tried with the precomputed method too and it didn't result in any BAM files either.

[fgponce]

Yeah thats a bit of a bugger. I ended up mapping them seperatelay to the pipeline with minimap2. Was a little bit annoying. I did try dredge the bams from the work directory but wasn't 100% sure I had complete versions of them. Some file sizes didn't seem the correct size.

[sarahjeeeze]

Hi, Sorry for this, it was not done intentionally. Thanks for letting us know, we will ensure the BAM's are available in the output again in the next release and let you know when this is ready.