Hi all,
I'm running pbsv in multisample mode providing a list of *.svsig.gz files of all my 180 samples trough a list.
I'm using this command
pbsv call \ --hifi -m 50 --max-ins-length 100K -j "$thr" \ "$REF" \ pbsv_pbmm2_nippo_multisample.fofn \ multisample.nippo.pbmm2.pbsv.vcf
The thing is that even if the job seems to start without error and using all the cores I'm giving to software (50 in this case) creating a VCF with all the sample names inside, after a couple of hours it will start to use only one core and literally get stuck for at least one month on that part (whatever it is; I have no message of error from the software). I do not even ever see an output because at that point my administrator has to reboot the workstation; and I tried on different workstation. So I cannot understand if the program itself is very poorly optimized or if it has some problem (that he "doesn't want to tell me"). But I guess is more linked to the first part. I'm trying the latest version of the software, 2.9.0. If you have any suggestions, please let me know. Thanks.
Hi all, I'm running pbsv in multisample mode providing a list of *.svsig.gz files of all my 180 samples trough a list. I'm using this command
pbsv call \ --hifi -m 50 --max-ins-length 100K -j "$thr" \ "$REF" \ pbsv_pbmm2_nippo_multisample.fofn \ multisample.nippo.pbmm2.pbsv.vcf
The thing is that even if the job seems to start without error and using all the cores I'm giving to software (50 in this case) creating a VCF with all the sample names inside, after a couple of hours it will start to use only one core and literally get stuck for at least one month on that part (whatever it is; I have no message of error from the software). I do not even ever see an output because at that point my administrator has to reboot the workstation; and I tried on different workstation. So I cannot understand if the program itself is very poorly optimized or if it has some problem (that he "doesn't want to tell me"). But I guess is more linked to the first part. I'm trying the latest version of the software, 2.9.0. If you have any suggestions, please let me know. Thanks.