terminate called after throwing an instance of 'std::out_of_range'

[wzhangahas]

Quast report of merged_canu_hifiasm_hifi.fasta
N50 28033498

command: nucmer -l 100 -prefix out merged_canu_hifiasm_hifi.fasta merged_canu_nd_racon_ont_hifi.fasta delta-filter -r -q -l 10000 out.delta > out.rq.delta quickmerge -d out.rq.delta -q merged_canu_nd_racon_ont_hifi.fasta -r merged_canu_hifiasm_hifi.fasta -hco 5.0 -c 1.5 -l 26700000 -ml 50000 -p hifi-ont

Aborted with the following error:

0 quickmerge 1 -d 2 out.rq.delta 3 -q 4 merged_canu_nd_racon_ont_hifi.fasta 5 -r 6 merged_canu_hifiasm_hifi.fasta 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 26700000 13 -ml 14 50000 15 -p 16 hifi-ont ptg000002l ctg000520 1 ptg000002l -1 ctg000460 1 ptg000003l ptg000003l 1 tig00000255 1 ptg000010l ctg000440 1 ptg000010l 1 ptg000015l tig00000051 1 ptg000015l -1 tig00000007 1 ptg000020l ctg000210 1 ptg000020l 1 tig00000440 ctg000170 1 tig00000440 1 terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 3781500) > this->size() (which is 0) run_quickmerge.sh: line 3: 45293 Aborted (core dumped) quickmerge -d out.rq.delta -q merged_canu_nd_racon_ont_hifi.fasta -r merged_canu_hifiasm_hifi.fasta -hco 5.0 -c 1.5 -l 26700000 -ml 50000 -p hifi-ont Could you give me some advices to run quickmerge? Thanks, Best wishes, Wei

[mahulchak]

Could you share your delta file?

On Tue, Nov 16, 2021, 23:30 wzhangahas @.***> wrote:

Quast report of merged_canu_hifiasm_hifi.fasta N50 28033498

command: nucmer -l 100 -prefix out merged_canu_hifiasm_hifi.fasta merged_canu_nd_racon_ont_hifi.fasta delta-filter -r -q -l 10000 out.delta > out.rq.delta quickmerge -d out.rq.delta -q merged_canu_nd_racon_ont_hifi.fasta -r merged_canu_hifiasm_hifi.fasta -hco 5.0 -c 1.5 -l 26700000 -ml 50000 -p hifi-ont

Aborted with the following error:

0 quickmerge 1 -d 2 out.rq.delta 3 -q 4 merged_canu_nd_racon_ont_hifi.fasta 5 -r 6 merged_canu_hifiasm_hifi.fasta 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 26700000 13 -ml 14 50000 15 -p 16 hifi-ont ptg000002l ctg000520 1 ptg000002l -1 ctg000460 1 ptg000003l ptg000003l 1 tig00000255 1 ptg000010l ctg000440 1 ptg000010l 1 ptg000015l tig00000051 1 ptg000015l -1 tig00000007 1 ptg000020l ctg000210 1 ptg000020l 1 tig00000440 ctg000170 1 tig00000440 1 terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 3781500) > this->size() (which is 0) run_quickmerge.sh: line 3: 45293 Aborted (core dumped) quickmerge -d out.rq.delta -q merged_canu_nd_racon_ont_hifi.fasta -r merged_canu_hifiasm_hifi.fasta -hco 5.0 -c 1.5 -l 26700000 -ml 50000 -p hifi-ont Could you give me some advices to run quickmerge? Thanks, Best wishes, Wei

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[wzhangahas]

Dear Mahul Chakraborty, The attachments are the command and the delta files. Please help me to check the error. Thank you very much, Best wishes, Wei

At 2021-11-17 18:11:49, "Mahul Chakraborty" @.***> wrote:

Could you share your delta file?

On Tue, Nov 16, 2021, 23:30 wzhangahas @.***> wrote:

Quast report of merged_canu_hifiasm_hifi.fasta N50 28033498

command: nucmer -l 100 -prefix out merged_canu_hifiasm_hifi.fasta merged_canu_nd_racon_ont_hifi.fasta delta-filter -r -q -l 10000 out.delta > out.rq.delta quickmerge -d out.rq.delta -q merged_canu_nd_racon_ont_hifi.fasta -r merged_canu_hifiasm_hifi.fasta -hco 5.0 -c 1.5 -l 26700000 -ml 50000 -p hifi-ont

Aborted with the following error:

0 quickmerge 1 -d 2 out.rq.delta 3 -q 4 merged_canu_nd_racon_ont_hifi.fasta 5 -r 6 merged_canu_hifiasm_hifi.fasta 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 26700000 13 -ml 14 50000 15 -p 16 hifi-ont ptg000002l ctg000520 1 ptg000002l -1 ctg000460 1 ptg000003l ptg000003l 1 tig00000255 1 ptg000010l ctg000440 1 ptg000010l 1 ptg000015l tig00000051 1 ptg000015l -1 tig00000007 1 ptg000020l ctg000210 1 ptg000020l 1 tig00000440 ctg000170 1 tig00000440 1 terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 3781500) > this->size() (which is 0) run_quickmerge.sh: line 3: 45293 Aborted (core dumped) quickmerge -d out.rq.delta -q merged_canu_nd_racon_ont_hifi.fasta -r merged_canu_hifiasm_hifi.fasta -hco 5.0 -c 1.5 -l 26700000 -ml 50000 -p hifi-ont Could you give me some advices to run quickmerge? Thanks, Best wishes, Wei

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[matt-shenton]

Thanks for this tool. I suspect that this error (I just encountered a similar one) may be caused by running more than one quickmerge job in the same directory. Files named "hybrid_oneline.fa" and "self_oneline.fa" are created at the beginning. If you start another job they will be overwritten, maybe causing this error. It wou;ld be good if these files got different names in an updated release. Best wishes Matt Shenton

[mahulchak]

@jgbaldwinbrown thoughts on this feature request?

[jgbaldwinbrown]

Sure, it's a pretty minor change to the script to use a randomly-generated or user-supplied filename and avoid this problem. I'll work on this change as soon as I can.

[jgbaldwinbrown]

Okay, pushed a fix for this. The hybrid and self oneline-fasta files should now use the same output prefix as other files in the pipeline, preventing name collisions in multiple runs in the same directory (as long as each has a unique prefix).

[matt-shenton]

Thanks!