Something wrong when I run until “Computing best solutions for UserReplicon ”

[gjzheng]

the log： ######### Hits analysis for replicon UserReplicon ########## Check model defense-finder-models/DefenseFinder_5/Aditi/Aditi Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX_I Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX_II Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX_III Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX_IV Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX_V Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/BREX/BREX_VI Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Borvo/Borvo Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Bunzi/Bunzi Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/CBASS/CBASS Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/CBASS/CBASS_I Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/CBASS/CBASS_II Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/CBASS/CBASS_III Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/CBASS/CBASS_IV Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Dazbog/Dazbog Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Eleos/Eleos Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Olokun/Olokun Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/PfiAT/PfiAT Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Pycsar/Pycsar Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_II Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_III Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_IV Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_IX Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_I_A Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_I_B Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_I_C Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_V Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_VI Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_VIII Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_VII_1 Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_VII_2 Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_X Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_XI Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_XII Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Retron/Retron_XIII Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/RnlAB/RnlAB Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/SEFIR/SEFIR Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/SanaTA/SanaTA Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/SoFIC/SoFic Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Tiamat/Tiamat Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/Uzume/Uzume Building clusters Searching systems Check model defense-finder-models/DefenseFinder_5/pAgo/pAgo Building clusters Searching systems  ###################### Computing best solutions ###################### Computing best solutions for UserReplicon (nb of candidate systems 240)

[SenyuanGu]

Hi, did you figure it out? I came up with the same issue with you... The program stucked in this step for a long time.

[jsweagley]

I am just bumping this thread because I have a similar issue with a handful of my files. I am running the current version of defense-finder on .faa protein files generated by Produigal on a cluster, each job has 24 CPUs devoted to it, and they have been running for over 1 day and 14 hours. A majority of the time it has been hung on this step, the last edit to the macsysfinder log files was within 15 minutes of the job starting.

Looking into the log files, it looks like DF_[1-5] and RM reached the END, only the log in /cas/ is stuck An example for one of the run says:

###################### Computing best solutions ###################### INFO : Computing best solutions for 160-01.meta.genes (nb of candidate systems 80)

For the stuck jobs, it looks like the 'nb of candidate systems' ranges from 76-85. Does the time to compute the best solution for Cas scale exponentially with the nb of candidate systems? I didn't record the nb of candidate systems for the runs that finished to determine how this relates to run time. Is there a --log-level (or --preserve-raw) parameter setting I could use to store the 'nb of candidate systems' if I rerun these to check the relationship?

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