Open weishwu opened 6 months ago
This contains the reference files I'm using:
This test run completed successfully:
nextflow run epi2me-labs/wf-metagenomics --fastq test_data/case04_exclude_host/reads.fastq.gz --exclude_host test_data/case04_exclude_host/host.fasta.gz
Hi @weishwu ,
First of all, thank you for using the workflow! I'll take a look to try to reproduce your issue. The error you are getting may be related to the use of the flag --minimap2_by_reference
.
While I investigate this and take a look on the databases files, are you able to run the workflow with your data but without that flag successfully to make sure it is the use of this flag which is causing trouble (as I've seen from you report, you have run successfully the demo)?
Thank you very much!
@nggvs
Thanks! It worked after I removed --minimap2_by_reference
.
However, I added this flag in order to get the coverage on each individual sequence in my reference. My reference contains the wzi gene sequence for 741 Klebsiella pneumonia strains, and the goal of this analysis is to find out the abundance of each strain. The resolution of the pipeline can only get down to species. Is there a way to accommodate the pipeline to my needs?
Since I got the BAM, I actually ran mosdepth
to get the coverage on each of the 741 sequences in my reference. Do you think I can rely on this data for the abundance measurement? My major concern is that minimap2 may be not aligning the reads to the correct one if some of these sequences are very close to each other (though I only used the alignments with mapping quality >0).
Thanks again.
Hi @weishwu ,
Apologies for the late answer, to see how alignments are working, assuming you have a reference on what you expect to find in the sample, you can use the latest version of the EPI2ME Desktop Application (5.1.14). Running minimap2 with the option keep bam
, will enable the IGV panel in the app so you can take a look on the alignments
Operating System
Other Linux (please specify below)
Other Linux
RedHat 7.9 (Maipo)
Workflow Version
v2.9.0-gd9e8593
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
export NXF_SINGULARITY_CACHEDIR=./env/nextflow_singularity_images/ export MPLCONFIGDIR=./outputs/wf_metagenomics/KP4/mplconfigdir/
nextflow run epi2me-labs/wf-metagenomics \ --fastq KP4.pass.filt.fastq \ --classifier minimap2 \ --sample KP4 \ --reference 741_wzi_types.fa \ --ref2taxid 741_wzi_types.ref2taxid.tab \ --keep_bam \ --minimap2_by_reference \ --out_dir wf_metagenomics/KP4 \ --threads 40 \ -profile singularity \ -c ${nf_conf}
Workflow Execution - CLI Execution Profile
singularity
What happened?
Got an error:
Relevant log output