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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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HELP!!!!!!terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_S_construct null not valid #44

Open sneupane01 opened 4 years ago

sneupane01 commented 4 years ago

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 commented 4 years ago

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

On Thu, Oct 3, 2019 at 1:15 PM sneupane01 notifications@github.com 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

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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

sneupane01 commented 4 years ago

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

mahulchak commented 4 years ago

Please send it to mchakrab[at]uci.edu

On Thu, Oct 3, 2019 at 1:48 PM sneupane01 notifications@github.com wrote:

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

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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

bnwaweru commented 4 years ago

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 commented 4 years ago

what is the source of the error

mahulchak commented 4 years ago

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 notifications@github.com wrote:

what is the source of the error

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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

sneupane01 commented 4 years ago

I sent my files though email.