segment fault and Core dump

[longzhangnation]

Hi ,
I am using two asseblies for one genome to quickmerge. The first one's size is 4Gb ， and its contigs number is 15k , the other's size is 5Gb ,and contigs number is 77k . When I use the first one as reference , and the second as query , quickmerge works fine . But when I use the first as query , the second as reference , it repeorts " segement fault ( core dump ) " and exit , no more information is reported . Could it be caused by the insufficient memory ? or anything else ? How can I work aroud ? here is the time -v to check the run ,

Command being timed: "./test.sh"
User time (seconds): 43.70
System time (seconds): 12.62
Percent of CPU this job got: 91%
Elapsed (wall clock) time (h:mm:ss or m:ss): 1:01.75
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 10218256
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 2620229
Voluntary context switches: 6
Involuntary context switches: 653
Swaps: 0
File system inputs: 0
File system outputs: 22312
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 139

[mahulchak]

Did you check if you are using the same delta file for both merging?

…

On Wed, Dec 23, 2020, 18:38 longzhangnation ***@***.***> wrote: Hi , I am using two asseblies for one genome to quickmerge. The first one's size is 4Gb ， and its contigs number is 15k , the other's size is 5Gb ,and contigs number is 77k . When I use the first one as reference , and the second as query , quickmerge works fine . But when I use the first as query , the second as reference , it repeorts " segement fault ( core dump ) " and exit , no more information is reported . Could it be caused by the insufficient memory ? or anything else ? How can I work aroud ? here is the time -v to check the run , Command being timed: "./test.sh" User time (seconds): 43.70 System time (seconds): 12.62 Percent of CPU this job got: 91% Elapsed (wall clock) time (h:mm:ss or m:ss): 1:01.75 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 10218256 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 2620229 Voluntary context switches: 6 Involuntary context switches: 653 Swaps: 0 File system inputs: 0 File system outputs: 22312 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 139 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#61>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZQH2ER632OGSDBMMZTGMTSWKSSDANCNFSM4VHV5EJA> .

[longzhangnation]

Maybe not . I rerun the second step , delta-filter with -l 20000, and do quickmerge again , it runs successfully and outputs the results . Maybe too many alignments caused the software unable to work .

[longzhangnation]

I use the original delta-filter result for quickemerge with parameter -ml 25000 ( at first using -m 10000 ) , and get the result ,too.