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rvicedomini / strainberry

Automated strain separation of low-complexity metagenomes
MIT License
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error: read mapping to strain-separated scaffolds failed #12

Open RolandFaure opened 11 months ago

RolandFaure commented 11 months ago

Hi,

I'm having trouble running one particular instance of Strainberry. If fails after giving me this message:

[M::mm_idx_gen::1.093*0.54] collected minimizers
[M::mm_idx_gen::1.184*1.20] sorted minimizers
[M::main::1.184*1.20] loaded/built the index for 616 target sequence(s)
[M::mm_mapopt_update::1.243*1.19] mid_occ = 91
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 616
[M::mm_idx_stat::1.276*1.18] distinct minimizers: 1564794 (73.57% are singletons); average occurrences: 1.575; average spacing: 5.253
[M::worker_pipeline::71.995*11.64] mapped 33507 sequences
[M::worker_pipeline::94.738*10.98] mapped 33617 sequences
[M::worker_pipeline::138.807*12.40] mapped 33156 sequences
[M::worker_pipeline::169.663*12.53] mapped 33569 sequences
[M::worker_pipeline::204.459*10.83] mapped 29349 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -t 16 assembly_flye.fa reads.fq
[M::main] Real time: 204.538 sec; CPU: 2214.816 sec; Peak RSS: 3.902 GB
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
[2023-10-05 09:30:33] Starting Strainberry v1.1
[2023-10-05 09:30:33] ### performing 2-strain separation
[2023-10-05 09:30:33] SNP calling and phasing
[2023-10-05 13:26:41] average Hamming ratio improved to 0.1967
[2023-10-05 13:26:41] separating reads
[2023-10-05 13:29:58] assembling strain haplotypes
[2023-10-05 16:18:38] scaffolding
[2023-10-05 16:22:00] mapping reads to strain-separated scaffolds
[2023-10-05 16:23:53] error: read mapping to strain-separated scaffolds failed

The command line used to launch Strainberry: /groups/genscale/rfaure/softs/strainberry/strainberry -r assembly_flye.fa -b reads_on_assembly.bam -o /groups/genscale/rfaure/Hairsplitter/10_Ecoli/nb_strain_5/10/sberry_out2 -c 16 -n 10

All the other instances of Strainberry I launched following a similar protocol worked fine, so I suspect a weird case happening just here. Do you have any idea where this could come from ?

Thanks :-) Roland

RolandFaure commented 11 months ago

Update: I re-ran the same dataset and it did not fail. The only thing that changed was that I used only 4 threads instead of 16... Problem solved on my end :-), you can close the issue if you want