Open KatrinMoller opened 3 weeks ago
etycksen
commented
2 weeks ago 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
commented
2 weeks ago @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:
fgponce
commented
2 weeks ago 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
commented
2 weeks ago @fgponce I actually tried with the precomputed method too and it didn't result in any BAM files either.
fgponce
commented
2 weeks ago 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
commented
1 week ago 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.
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
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