EXCEPTION: cannot open ./trashme_3684_dsk_partitions_gatb/parts.360

[githubgig]

Hello,

I previously ran DiscoSnp (reference free) with c 3, k31, b0, no low complexity successfully, but the genotyping rate is very low 0.036 after filtering. I tried changing to k51 and b1 to try to improve that, but I'm getting the below error. Why is the genotyping rate so low in the first run and what can I do to improve it? How can I try different parameters without getting this error? I can see the folder _trashme_3684_dsk_partitionsgatb was created, but the run has crashed.

[DSK: Pass 1/2, Step 1: partitioning ] 25 % elapsed: 207 min 7 sec remaining: 621 min 22 sec cpu: 686.9 % mem: [2744, 2744, 2744] MB Error: can't create output directory (./trashme_3684_dsk_partitions_gatb/) debug, doesexist:0created directory ./trashme_3684_dsk_partitions_gatb/

EXCEPTION: cannot open ./trashme_3684_dsk_partitions_gatb/parts.360 Too many open files there was a problem with graph construction$ reset

Thanks.

[pierrepeterlongo]

Hi

• Can you please precise what you mean by genotyping rate?
• About the issue with the number of opened files: please check links such as. https://www.baeldung.com/linux/error-too-many-open-files.

Pierre

[githubgig]

Hi Pierre,

Its the proportion of genotypes present per marker (here only 0.036 or 3.6% are present), which basically means 0.964 (or 96.4%) of data is missing. The total would probably be the average/mean across all markers.

[pierrepeterlongo]

So I understand you expect to find a set of markers but you're finding only a tiny portion of them, right? In this case, you may try less stringent parameters

• run with -b2 (in this case no need to recompute the graph, you may use the graph produced by your first successful run as input).
• run with more SNPs per bubble (idem, do not recompute the graph)
• depending on your input data, you may also reduce the solidity threshold (in this case you need to recompute the graph).

[pierrepeterlongo]

I close this issue - please reopen it if your question was not answered in May.