Command terminated by signal 11

[lt11]

Hi All,

I get an error while running pggb on 15 saccharomyces assemblies:

[smoothxg::create_consensus_graph] cleaning up redundant link paths
Command terminated by signal 11
smoothxg -t 132 -g /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.seqwish.gfa -w 10000 -I 0 -j 5000 -e 5000 -l 10000 -m /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.smooth.maf -s /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.consensus -a -C 10,100,1000,10000 -o /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.smooth.gfa
32771.07s user 727.37s system 2672% cpu 1253.48s total 20854404Kb max memory

Everything works fine if I reduce the number of assemblies (e.g. to 7).

I'm using a server with ~500 GB RAM, 176 cores, more than 10 TB of free temporary HDD storage.

Any suggestion?

Best,

Lorenzo

[ekg]

We are about to make a release. Would you mind trying again with the updated version of the pipeline?

…

On Thu, Dec 17, 2020, 19:27 Lorenzo Tattini ***@***.***> wrote: Hi All, I get an error while running pggb on 15 saccharomyces assemblies: [smoothxg::create_consensus_graph] cleaning up redundant link paths Command terminated by signal 11 smoothxg -t 132 -g /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.seqwish.gfa -w 10000 -I 0 -j 5000 -e 5000 -l 10000 -m /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.smooth.maf -s /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.consensus -a -C 10,100,1000,10000 -o /data/cp-full/multisaccha-prefix.fa.gz.pggb-s50000-p70-n10-a70-K16-k8-w10000-j5000-e5000-I0.smooth.gfa 32771.07s user 727.37s system 2672% cpu 1253.48s total 20854404Kb max memory Everything works fine if I reduce the number of assemblies (e.g. to 7). I'm using a server with ~500 GB RAM, 176 cores, more than 10 TB of free temporary HDD storage. Any suggestion? Best, Lorenzo — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#47>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEPSKGG7LKWQ63HWKULSVJERPANCNFSM4VAB2R7Q> .

[lt11]

Hi All,

Any news about this thread?

Best,

Lorenzo

[AndreaGuarracino]

Hi Lorenzo, several issues regarding time and memory usage have been fixed in the last few weeks. A little more patience, we will release a new version soon. Sorry for the delay.

[lt11]

Thanks guys! Looking forward for the new release!

[lt11]

Problem solved with the latest updates!

[ekg]

Nice!

…

On Mon, Jan 25, 2021 at 12:37 PM Lorenzo Tattini ***@***.***> wrote: Problem solved with the latest updates! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEOP6OAFYZFWZO3ORYLS3VJYPANCNFSM4VAB2R7Q> .

[AndreaGuarracino]

@lt11, thank you for confirming it.