Open MarieLataretu opened 2 years ago
Hi Marie, would you be able to check how much coverage amplicon 51 has? If it has coverage below the threshold that would suggest that the pipeline is failing because the output file isn't being produced for that amplicon, however with "-k" snakemake should just carry on regardless. It would be useful to know if that is the source of the problem.
Are there any files that have been output in the split/ folder when it fails?
Hi :)
yes, in the split folder are several ampliconXX.fastq files, but the one snakemake looks for is indeed missing.
I noticed, that it's always about unclassified reads - I guess it's smarter to input only classified (barcoded) reads 😅 I'll keep you updated!
Could you have a try with the attached version of Lilo and let me know if it gets past that point?
It shouldn't be necessary, I have it running on very gappy SARS-CoV-2s right now, but in this version if there are no reads for the amplicon it creates an empty fastq file.
Yep, it was not the unclassified reads. I'll try the new version :)
Maybe you can also check on my primer input (ARTIC V4.1) nCoV-2019.V4.1.primer.csv nCoV-2019.V4.1.noalt.scheme.bed.txt
I have just tested your input files on my data and they work perfectly, so it isn't that.
Are you using the version of snakemake from the conda environment? The only reason I can think it wouldn't be working is snakemake is for some reason ignoring the -k telling it not to worry about low coverage amplicons that don't produce output. Is there anything in your --profile configuration for slurm that would overwrite that?
I updated snakemake at some point to 6.15.5
to see if it makes a difference.
In my config is keep-going
true and it's also explicitly called with -k
🤔
Can you check what happens when you run the command that it says failed?
i.e.:
bedtools intersect -F 0.9 -wa -wb -bed -abam FAR95540_pass_unclassified_7f618209_73/alignments/reads_to_ref.bam -b amplicons.bed | grep amplicon51 - | awk '{print $4}' - | seqtk subseq porechop/FAR95540_pass_unclassified_7f618209_73.fastq.gz - > FAR95540_pass_unclassified_7f618209_73/split/amplicon51.fastq
Hi there,
I'm trying to run LILO on a SLURM HPC and I'm not sure what the errors are related to. Do you have an idea? It seems really environment depended, but maybe you stumbled across something similar.
Call:
Log:
I set
--latency-wait 90
it again breaks after some time at aassign
rule and aKeyError: read_select
from the snakemake scheduler.Let me know which input/config files might be interesting to solve this. :)