rob-p
commented
1 year ago Hi @charlesfoster,
Thanks for opening the issue. The second run looks like it ends before there is any information about mapped reads. Have mappings started to be reported at that point? I wonder if there is some issue related to the loading of the index. I have a few suggestions that may be worthwhile to try:
1) Do you observe the same problem if you index only the transcriptome (i.e. if you don't also include the genome as a decoy)?
2) If you are using nfcore/rnaseq you can also consider using the STAR => salmon path. Of course, I'm interested in addressing whatever the underlying issue here is anyway, but it's worth noting that this may be a viable alternative to allow you to process all of these samples using the nfcore pipeline in the meantime. This will align the reads to the genome using STAR (which gives the benefit of having a full decoy), project them to the transcriptome, and then quantify them.
Also, if you can share a set of problematic reads (or even a subset of them that will reproduce the extreme slowness problem) privately, that would be very helpful in debugging. In addition to trying to debug what's going on here, I'd probably also try running them through piscem. While this isn't yet an actual substitute for salmon, it will help isolate if the problem is directly related to the index or something else.
Thanks! Rob
charlesfoster
Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? salmon
Describe the bug I'm working with 15 samples, with ~5Gb total reads per sample (90,000,000 to 100,000,000 reads, ~75 bp reads). I've tried running these samples through the
nf-core/rnaseqpipeline, but the pipeline took an age to run before dying at thesalmon quantsteps. Some samples finished in about 12 minutes. Others timed out after 8+ hours.(taken from the terminal as the logfile is empty, and the current time is 12:54 pm = >3 hr run time so far)
To Reproduce I ran the following command:
nf-core/rnaseq: via singularity; while running manually to troubleshoot: conda.Expected behavior All samples with similar numbers of reads using the same index to finish in roughly the same amount of time.
Screenshots If applicable, add screenshots or terminal output to help explain your problem.
Desktop (please complete the following information):
$lsb_release -a No LSB modules are available. Distributor ID: Pop Description: Pop!_OS 22.04 LTS Release: 22.04 Codename: jammy
kallisto index -i transcripts.idx genome.transcripts.fa kallisto quant -i transcripts.idx -o output -b 100 <(zcat ${R1}) <(zcat ${R2}) -t 6