HELP!!!!!!terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_S_construct null not valid

[sneupane01]

quickmerge -d out.rq_1.delta -q /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/uni_corrected/assembly_edited.fasta -r /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/wDi.contigs.fasta_headeredited_spaceremoved.fa -hco 5.0 -c 1.5 -l 1250000 -ml 10000

0 quickmerge
1 -d
2 out.rq_1.delta
3 -q
4 /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/uni_corrected/assembly_edited.fasta
5 -r
6 /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/wDi.contigs.fasta_headeredited_spaceremoved.fa
7 -hco
8 5.0
9 -c
10 1.5
11 -l
12 1250000
13 -ml
14 10000
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string::_S_construct null not valid
Aborted

[mahulchak]

Hi, do the sequence names in your delta file and fasta files match?

…

On Thu, Oct 3, 2019 at 1:15 PM sneupane01 ***@***.***> wrote: quickmerge -d out.rq_1.delta -q /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/uni_corrected/assembly_edited.fasta -r /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/wDi.contigs.fasta_headeredited_spaceremoved.fa -hco 5.0 -c 1.5 -l 1250000 -ml 10000 0 quickmerge 1 -d 2 out.rq_1.delta 3 -q 4 /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/uni_corrected/assembly_edited.fasta 5 -r 6 /ufrc/pelzstelinski/sneupane/Analysis_of_Demultiplexed_10_wDi_DNA_HMW_Unpure_1st_Elution/wDi_canu_seqtk45_CCS_1000_corr0.015_500_100_GOOD/wDi.contigs.fasta_headeredited_spaceremoved.fa 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 1250000 13 -ml 14 10000 terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_S_construct null not valid Aborted — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#44?email_source=notifications&email_token=ABZQH2EQRPYNVHYXY35UFXDQMZGTDA5CNFSM4I5HVRP2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HPQCKVA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZQH2BVCAGGP6ZQGDGR633QMZGTDANCNFSM4I5HVRPQ> .

-- 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

[sneupane01]

Can I send you my reference and query files? Let me know your email add.

[mahulchak]

Please send it to mchakrab[at]uci.edu

…

On Thu, Oct 3, 2019 at 1:48 PM sneupane01 ***@***.***> wrote: Can I send you my reference and query files? Let me know your email add. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#44?email_source=notifications&email_token=ABZQH2FXUXL3MBH5556MQALQMZK4ZA5CNFSM4I5HVRP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAJRLSY#issuecomment-538121675>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZQH2GMQDVCZVUGYFLQ3PDQMZK4ZANCNFSM4I5HVRPQ> .

-- 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

[bnwaweru]

Hello am running quickmerge, the nucmer step runs fine but the delta-filter step fails, here is the error log

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "flye_wtdbg2_merge.ntref" of length 367767617

construct suffix tree for sequence of length 367767617

(maximum reference length is 2305843009213693948)

(maximum query length is 18446744073709551615)

process 3677676 characters per dot

#....................................................................................................

CONSTRUCTIONTIME /export/apps/MUMmer/3.23/mummer flye_wtdbg2_merge.ntref 584.20

reading input file "test_1.raw.fa" of length 337748768

matching query-file "test_2.raw.fa"

against subject-file "flye_wtdbg2_merge.ntref"

COMPLETETIME /export/apps/MUMmer/3.23/mummer flye_wtdbg2_merge.ntref 1805.34

SPACE /export/apps/MUMmer/3.23/mummer flye_wtdbg2_merge.ntref 681.96

4: FINISHING DATA

USAGE: delta-filter [options]

Try 'delta-filter -h' for more information.
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string::_S_construct null not valid
/tmp/slurmd/job27774/slurm_script: line 34: 26788 Aborted (core dumped) quickmerge -d flye_wtdbg2_merge.rq.delta -q test_2.raw.fa -r test_1.fasta -hco 5.0 -c 1.5 -l 470233 -ml 10000

[bnwaweru]

what is the source of the error

[mahulchak]

I think the delta-filter command is not specified correctly. What are your nucmer and delta-filter commands?

…

On Fri, Oct 4, 2019 at 5:39 AM bwaweru ***@***.***> wrote: what is the source of the error — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#44?email_source=notifications&email_token=ABZQH2CSABABBZ2FDK6KHODQM42M3A5CNFSM4I5HVRP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEALQIIQ#issuecomment-538379298>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZQH2BSX524W7W7OHA2SSTQM42M3ANCNFSM4I5HVRPQ> .

-- 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

[sneupane01]

I sent my files though email.