Segmentation fault (core dumped)

[shishuo16]

Segmentation fault (core dumped) svmu test.50.delta human.fa human.cor.fa 10 h > nh.small.txt How so?

[shishuo16]

Also, I run /usr/bin/time -v svmu test.10.delta chr1.fa human.cor.fa 1 l > nh.small.txt & Command being timed: "svmu test.10.delta chr1.fa human.cor.fa 1 l" User time (seconds): 9.21 System time (seconds): 1.47 Percent of CPU this job got: 91% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:11.66 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): 1119184 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 30610 Voluntary context switches: 158650 Involuntary context switches: 15 Swaps: 0 File system inputs: 0 File system outputs: 40 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0

[1]+ Exit 11 /usr/bin/time -v svmu test.10.delta chr1.fa human.cor.fa 1 l > nh.small.txt

[mahulchak]

Did you get any output ? E.g. in the small.txt or sv.txt ? Do you have a core. file ( is any number)? If you have the coredump file then you could run the following and send me the output (* is a number):

gdb svmu core.*

On Mon, Apr 16, 2018 at 1:39 PM shishuo16 notifications@github.com wrote:

Also, I run /usr/bin/time -v svmu test.10.delta chr1.fa human.cor.fa 1 l

nh.small.txt & Command being timed: "svmu test.10.delta chr1.fa human.cor.fa 1 l" User time (seconds): 9.21 System time (seconds): 1.47 Percent of CPU this job got: 91% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:11.66 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): 1119184 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 30610 Voluntary context switches: 158650 Involuntary context switches: 15 Swaps: 0 File system inputs: 0 File system outputs: 40 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0

[1]+ Exit 11 /usr/bin/time -v svmu test.10.delta chr1.fa human.cor.fa 1 l

nh.small.txt

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[liufy11]

when I run my data with the command: ~/Biosoft/svmu-0.3-alpha/svmu test.delta ~/Test/Ref/Brassica_napus/Brassica_napus_v4.1.chromosomes.fa test.fasta 50 l I meet with the same problem "Segmentation fault (core dumped)" I get the files, namely :cnv_all.txt、cords.txt、indel.txt、small.txt、sv.txt but there's little or none content in the files above . I don't know what's wong. I want to search for big insert that is above 500bp in my test.fasta , I don't know what to do ? Can I realize my goal with svmu ?

[mahulchak]

Did you obtain the copy using git clone? if you haven't may be try that? If you still encounter the issue, then it will be easier for me to look into.

On Thu, Apr 18, 2019 at 6:20 AM liufy11 notifications@github.com wrote:

when I run my data with the command: ~/Biosoft/svmu-0.3-alpha/svmu test.delta ~/Test/Ref/Brassica_napus/Brassica_napus_v4.1.chromosomes.fa test.fasta 50 l I meet with the same problem "Segmentation fault (core dumped)" I get the files, namely :cnv_all.txt、cords.txt、indel.txt、small.txt、sv.txt but there's little or none content in the files above . I don't know what's worry. I want to search for big insert that is bigger than 500bp in my test.fasta , I don't know what to do ? Can I realize my goal with svmu ?

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-- Mahul Chakraborty Department of Ecology and Evolutionary Biology University of California-Irvine Phone: 949 824 9559 Fax: 949 824 9559 Github: https://github.com/mahulchak