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mahulchak / quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
GNU General Public License v3.0
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segment fault and Core dump #61

Open longzhangnation opened 3 years ago

longzhangnation commented 3 years ago

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 commented 3 years ago

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

On Wed, Dec 23, 2020, 18:38 longzhangnation notifications@github.com 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

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longzhangnation commented 3 years ago

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 commented 3 years ago

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