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Hi, interested in using BinSanity, thanks for your hard work in developing/maintaining it.
I'm using Binsanity v0.4.1, installed with conda.
When running my metagenomes on cluster nodes with 400gb of RAM, they failed so I'm trying to run Binsanity-lc. I used these parameters, again with 20 processors and 400gb of RAM:
It looks like the kmeans step completes but in the Affinity Propagation stage it fails:
____________________________________________________ Clustering Bin SD01cat-kmean-bin_71.fna via Affinity Propagation ____________________________________________________ Preference: -3 Maximum Iterations: 4000 Convergence Iterations: 400 Contig Cut-Off: 3000 Damping Factor: 0.95 Coverage File: /storage/home/hcoda1/0/mwoodworth8/scratch/PREMIX/21.01.01_all_metagenomes/06.h.binsanity_pt_cat/profiles/SD01cat.cov.cov.x100.lognorm Fasta File: SD01cat-kmean-bin_71.fna Output Directory: /storage/home/hcoda1/0/mwoodworth8/scratch/PREMIX/21.01.01_all_metagenomes/06.h.binsanity_pt_cat/SD01cat-BinsanityWF (47, 1)Traceback (most recent call last): File "/storage/home/hcoda1/0/mwoodworth8/.conda/envs/binsanity/bin/Binsanity-lc", line 516, in <module> print("The program failed to complete clustering with affinity propagation when it reached %s. Check the number of contigs in the following bin: %s. If the number is >100,000 it is likely you ran into a memory error.") % (clust)TypeError: not enough arguments for format string
I've attached the log file below. Are there thoughts on what could be going on here?
Its an interesting failure because based on what you log-file says its a small set of contigs its trying to cluster at the step its failing at. Historically when I have encountered failures at this stage it is due to memory issues. But one other issue that could be causing this that I have run into once before is related to contig ids. Specifically errors can arise when ids aren't simplified deflines or if contig ids start with a number.
So try normalizing your contig ids to read similar to:
Hi, interested in using BinSanity, thanks for your hard work in developing/maintaining it.
I'm using Binsanity v0.4.1, installed with conda.
When running my metagenomes on cluster nodes with 400gb of RAM, they failed so I'm trying to run Binsanity-lc. I used these parameters, again with 20 processors and 400gb of RAM:
Binsanity-lc -f ${indir} -l ${ID}_scaffolds.fasta -c ${pDIR}/profiles/${ID}.cov.cov.x100.lognorm -o ${pDIR}/${ID}-BinsanityWF -x 3000 --checkm_threads 20 --kmean_threads 20 --Prefix ${ID}
It looks like the kmeans step completes but in the Affinity Propagation stage it fails:
I've attached the log file below. Are there thoughts on what could be going on here?
thanks!
SD01cat-BinsanityLC-log.txt
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