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mahulchak
core dumped: terminate called after throwing an instance of 'std::invalid_argument'
Hello:
I had run quickmerge by the following commands:
nucmer -l 100 -prefix out contig.fasta pacbio_assemble.fasta
delta-filter -r -q -l 10000 out.delta > outrq.delta
quickmerge -d outrq.delta -q contig.fasta -r pacbio_assemble.fasta -hco 5 -c 1 -l n -ml m -p prefix
But in the third steps, I got an error，and nothing carry out. lIKE THIS:
n -ml m -p prefix 0 quickmerge 1 -d 2 yylrq.delta 3 -q 4 /mnt/data/liyunxia/4-project/mito/YYL_Mtctgs-zhu2-uniq.fasta 5 -r 6 /mnt/data/liyunxia/4-project/mito/Mashmap/fmap/YYL.pass.fa@fmlrcor@mashmap2-idseq 7 -hco 8 5 9 -c 10 1 11 -l 12 n 13 -ml 14 m 15 -p 16 prefix terminate called after throwing an instance of 'std::invalid_argument' what(): stoi Aborted (core dumped)
I check the gdb -c core.317488, and I got this one:
Missing separate debuginfo for the main executable file Try: yum --enablerepo='debug' install /usr/lib/debug/.build-id/9a/5d301e005e22924e5bf88f3b95641c2490a441 Core was generated by `quickmerge -d out.delta -q /pwd/contig.fasta'. Program terminated with signal 6, Aborted. #0 0x00007fe7c0ef2207 in ?? () (gdb) where #0 0x00007fe7c0ef2207 in ?? () #1 0x00007fe7c0ef38f8 in ?? () #2 0x0000000000000020 in ?? () #3 0x0000000000000000 in ?? ()
So, what‘s’ the problems with this run? Hope for your reply.
You have replace 'n' and 'm' in the command line by actual integers. Please see the README. Also, I would suggest not to use c less than 1.5 (you have used 1)
On Wed, Oct 16, 2019 at 2:32 AM Yunxia-li [email protected] wrote:
Hello: I had run quickmerge by the following commands: nucmer -l 100 -prefix out contig.fasta pacbio_assemble.fasta delta-filter -r -q -l 10000 out.delta > outrq.delta quickmerge -d outrq.delta -q contig.fasta -r pacbio_assemble.fasta -hco 5 -c 1 -l n -ml m -p prefix But in the third steps, I got an error，and nothing carry out. lIKE THIS:
n -ml m -p prefix 0 quickmerge 1 -d 2 yylrq.delta 3 -q 4 /mnt/data/liyunxia/4-project/mito/YYL_Mtctgs-zhu2-uniq.fasta 5 -r 6 /mnt/data/liyunxia/4-project/mito/Mashmap/fmap/YYL.pass.fa@fmlrcor @mashmap2-idseq 7 -hco 8 5 9 -c 10 1 11 -l 12 n 13 -ml 14 m 15 -p 16 prefix terminate called after throwing an instance of 'std::invalid_argument' what(): stoi Aborted (core dumped)
I check the gdb -c core.317488, and I got this one:
Missing separate debuginfo for the main executable file Try: yum --enablerepo='debug' install /usr/lib/debug/.build-id/9a/5d301e005e22924e5bf88f3b95641c2490a441 Core was generated by `quickmerge -d out.delta -q /pwd/contig.fasta'. Program terminated with signal 6, Aborted. #0 0x00007fe7c0ef2207 in ?? () (gdb) where #0 0x00007fe7c0ef2207 in ?? () #1 https://github.com/mahulchak/quickmerge/issues/1 0x00007fe7c0ef38f8 in ?? () #2 https://github.com/mahulchak/quickmerge/issues/2 0x0000000000000020 in ?? () #3 https://github.com/mahulchak/quickmerge/issues/3 0x0000000000000000 in ?? ()
So, what‘s’ the problems with this run? Hope for your reply.
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Hi：
I first ran this, And it was successful.
merge_wrapper.py Mtctgs-zhu2-uniq.fasta YYL.pass.fa@fmlrcor@mashmap2-idseq
Then I tried this step by step:
1, nucmer -l 100 -prefix YYL_Mtctgs-zhu2-uniq Mtctgs-zhu2-uniq.fasta YYL.pass.fa@fmlrcor@[email protected] , result file: 100out.delta(50k)
2. delta-filter -r -q -l 10000 100out.delta > out.rq.delta (28k)
3. quickmerge -d out.rq.delta -q Mtctgs-zhu2-uniq.fasta -r YYL.pass.fa@fmlrcor@[email protected] -hco 5.0 -c 1.5 -l 5000 -ml 5000 -p prefix
But I got an error:
0 quickmerge 1 -d 2 1000out.rq.delta 3 -q 4 /mnt/data/liyunxia/4-project/mito/YYL_Mtctgs-zhu2-uniq.fasta 5 -r 6 /mnt/data/liyunxia/4-project/mito/Mashmap/fmap2/YYL.pass.fa@fmlrcor@[email protected] 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 500 13 -ml 14 500 15 -p 16 prefix NODE_158_length_51230_cov_66.467911 utg000051c 1 NODE_158_length_51230_cov_66.467911 1 NODE_8511_length_231609_cov_68.992912 utg000043c 1 NODE_8511_length_231609_cov_68.992912 1 terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr Aborted (core dumped)
How it comes?
Do you have white space in your fasta headers?
On Sun, Oct 20, 2019 at 8:48 PM Yunxia-li [email protected] wrote:
Hi：
I first ran this, And it was successful. merge_wrapper.py Mtctgs-zhu2-uniq.fasta YYL.pass.fa@fmlrcor@mashmap2-idseq
Then I tried this step by step: 1, nucmer -l 100 -prefix YYL_Mtctgs-zhu2-uniq Mtctgs-zhu2-uniq.fasta YYL.pass.fa@fmlrcor@[email protected] , result file: 100out.delta(50k) 2. delta-filter -r -q -l 10000 100out.delta > out.rq.delta (28k) 3. quickmerge -d out.rq.delta -q Mtctgs-zhu2-uniq.fasta -r YYL.pass.fa@fmlrcor@[email protected] -hco 5.0 -c 1.5 -l 5000 -ml 5000 -p prefix But I got an error:
0 quickmerge 1 -d 2 1000out.rq.delta 3 -q 4 /mnt/data/liyunxia/4-project/mito/YYL_Mtctgs-zhu2-uniq.fasta 5 -r 6 /mnt/data/liyunxia/4-project/mito/Mashmap/fmap2/YYL.pass.fa@fmlrcor@ [email protected] 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 500 13 -ml 14 500 15 -p 16 prefix NODE_158_length_51230_cov_66.467911 utg000051c 1 NODE_158_length_51230_cov_66.467911 1 NODE_8511_length_231609_cov_68.992912 utg000043c 1 NODE_8511_length_231609_cov_68.992912 1 terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr Aborted (core dumped)
How it comes?
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-- Mahul Chakraborty Department of Ecology and Evolutionary Biology University of California-Irvine Phone: 949 824 9559 Fax: 949 824 9559 Website: https://mahulchakraborty.wordpress.com/ Github: https://github.com/mahulchak