Even if the genome is small, shouldn't too many samples be added to build the graph about pggb HOT 8 OPEN

On Fri, Jun 30, 2023, 12:21 Wwwwwwwyc ***@***.***> wrote: Thanks for your help, we got back into running the pipeline and just came to the slow down part. We are running on a local HDD disk. Seqwish is slow down in the indexing process and the log file is as follows: [seqwish::seqidx] 0.000 indexing sequences [seqwish::seqidx] 40.197 index built [seqwish::alignments] 40.197 processing alignments [seqwish::alignments] 20878.751 indexing top NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 0 0.836t 0.831t 0.830t D 16.8 42.9 45082:29 seqwish The output file looks like this: 92K 4I3HBy.sqi 6.3G RmtjUs.sqq 845G vXXiRd.sqa Could this be because I aligned softmask genome? — Reply to this email directly, view it on GitHub <#316 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEK6GWGWG3NPJ2IPWDLXNZA47ANCNFSM6AAAAAAZWTPESQ> . You are receiving this because you commented.Message ID: ***@***.***>

On Fri, Jul 28, 2023, 09:39 Wwwwwwwyc ***@***.***> wrote: Hello! Sorry I'm bothering you again. This time we waited for the end of the procedure. We ran: pggb -i chr1_pan_filter_shorter_than_50k.fa -o chr1.pan -n 1589 -t 128 -p 90 -s 5000 -S -m -V ref:# but got the following error: [wfmash::skch::Map::mapQuery] mapped 100.00% @ 2.59e+06 bp/s elapsed: 00:00:43:05 remain: 00:00:00:00 [wfmash::skch::Map::mapQuery] count of mapped reads = 2225, reads qualified for mapping = 2228, total input reads = 2228, total input bp = 6704481258 [wfmash::map] time spent mapping the query: 2.59e+03 sec [wfmash::map] mapping results saved in: /dev/stdout wfmash -s 5000 -l 25000 -p 90 -n 1588 -k 19 -H 0.001 -X -t 128 --tmp-base chr1.pan chr1_pan_50k.fa --approx-map 322888.33s user 1654.82s system 12388% cpu 2619.72s total 19614516Kb max memory [wfmash::align] Reference = [chr1_pan_50k.fa] [wfmash::align] Query = [chr1_pan_50k.fa] [wfmash::align] Mapping file = chr1.pan/wfmash-1331Yx [wfmash::align] Alignment identity cutoff = 0.72% [wfmash::align] Alignment output file = /dev/stdout [wfmash::align] time spent loading the reference index: 0.164741 sec [wfmash::align::computeAlignments] aligned 100.00% @ 4.48e+07 bp/s elapsed: 01:07:41:59 remain: 00:00:00:00 [wfmash::align::computeAlignments] count of mapped reads = 2228, total aligned bp = 5109032990714 [wfmash::align] time spent computing the alignment: 1.14e+05 sec [wfmash::align] alignment results saved in: /dev/stdout wfmash -s 5000 -l 25000 -p 90 -n 1588 -k 19 -H 0.001 -X -t 128 --tmp-base chr1.pan chr1_pan_50k.fa -i chr1.pan/chr1_pan_50k.fa.ee441bc.mappings.wfmash.paf --invert-filtering 14407243.04s user 128933.60s system 12733% cpu 114153.25s total 14749796Kb max memory [seqwish::seqidx] 0.000 indexing sequences [seqwish::seqidx] 38.848 index built [seqwish::alignments] 38.848 processing alignments [seqwish::alignments] 23203.418 indexing [seqwish::alignments] 1714820.808 index built [seqwish::transclosure] 1714820.852 computing transitive closures [seqwish::transclosure] 1714823.517 0.00% 0-10000000 overlap_collect Command terminated by signal 9 seqwish -s chr1_pan_50k.fa -p chr1.pan/chr1_pan_50k.fa.ee441bc.alignments.wfmash.paf -k 19 -f 0 -g chr1.pan/chr1_pan_50k.fa.ee441bc.417fcdf.seqwish.gfa -B 10000000 -t 128 --temp-dir chr1.pan -P 4914907.12s user 80460.79s system 285% cpu 1750681.50s total 1269699096Kb max memory Does this seem to be caused by insufficient memory? We were confused because we had done partition and only had a sequence of about 5M per sample. Perhaps it is currently difficult to build graphs on samples of 1000 orders of magnitude? — Reply to this email directly, view it on GitHub <#316 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEL7TLO3TWOSGR6HLQLXSNUEXANCNFSM6AAAAAAZWTPESQ> . You are receiving this because you commented.Message ID: ***@***.***>