Aborted (core dumped) quickmerge

[chenzhaozhu]

1 -d
2 2020merge/out.rq.delta
3 -q
4 2020.fa
5 -r
6 pilon_polished.fasta
7 -hco
8 5.0
9 -c
10 1.5
11 -l
12 0
13 -ml
14 5000
15 -p
16 2020merge/2020.mfa
ptg000009l_pilon ptg000009l_pilon 1 JAAIVE010000736.1 1 ptg000536l_pilon -1
ptg000091l_pilon JAAIVE010000152.1 1 ptg000091l_pilon -1
ptg000199l_pilon ptg000199l_pilon 1 JAAIVE010000169.1 -1 ptg000755l_pilon -1
ptg000285l_pilon ptg000285l_pilon 1 JAAIVE010000015.1 -1 ptg001264l_pilon -1
ptg000294l_pilon JAAIVE010000686.1 1 ptg000294l_pilon 1
ptg000341l_pilon ptg000341l_pilon 1 JAAIVE010000429.1 -1 ptg000036l_pilon 1
ptg000547l_pilon ptg000547l_pilon 1 JAAIVE010000200.1 -1
ptg000565l_pilon ptg000565l_pilon 1 JAAIVE010000017.1 -1 ptg000682l_pilon 1
ptg001402l_pilon ptg001402l_pilon 1 JAAIVE010000003.1 1 ptg000326l_pilon 1
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr: __pos (which is 20474) > this->size() (which is 0)

[ziweiwuzw]

Hello, I meet same issue, are you figure out?

[mahulchak]

Can you please post your command?

…

On Wed, Jun 14, 2023, 03:42 Wu Ziwei ***@***.***> wrote: Hello, I meet same issue, are you figure out? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/mahulchak/quickmerge/issues/72*issuecomment-1590746790__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!Psz-wygMl3AGFdhw0Lv6ZlFnJf7ISs9fblQoPsvUEpkL93DrA3XHMYYW-JmIUJr01vrqGNSWaSv0P6xVLBD_Z-bv$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABZQH2FBRNRMGOY2F2S3U6LXLF2OHANCNFSM6AAAAAAWWHGYM4__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Psz-wygMl3AGFdhw0Lv6ZlFnJf7ISs9fblQoPsvUEpkL93DrA3XHMYYW-JmIUJr01vrqGNSWaSv0P6xVLGmAuFBf$> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[chenzhaozhu]

Yeah, I fixed it. The two files you compare cannot have the same name, and when using nucmer, the reference sequence is followed by the query sequence, which cannot be reversed when merging

…

--------------原始邮件-------------- 发件人："Wu&nbsp;Ziwei ***@***.***&gt;; 发送时间：2023年6月14日(星期三) 下午4:42 收件人："mahulchak/quickmerge" ***@***.***&gt;; 抄送："朱晨朝 ***@***.***&gt;;"Author ***@***.***&gt;; 主题：Re: [mahulchak/quickmerge] Aborted (core dumped) quickmerge (Issue #72) ----------------------------------- Hello, I meet same issue, are you figure out? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;

[chenzhaozhu]

Yeah, I fixed it. The two files you compare cannot have the same name, and when using nucmer, the reference sequence is followed by the query sequence, which cannot be reversed when merging

…

--------------原始邮件-------------- 发件人："Mahul&nbsp;Chakraborty ***@***.***&gt;; 发送时间：2023年6月15日(星期四) 上午6:30 收件人："mahulchak/quickmerge" ***@***.***&gt;; 抄送："朱晨朝 ***@***.***&gt;;"Author ***@***.***&gt;; 主题：Re: [mahulchak/quickmerge] Aborted (core dumped) quickmerge (Issue #72) ----------------------------------- Can you please post your command? On Wed, Jun 14, 2023, 03:42 Wu Ziwei ***@***.***&gt; wrote: &gt; Hello, I meet same issue, are you figure out? &gt; &gt; — &gt; Reply to this email directly, view it on GitHub &gt; <https://urldefense.com/v3/__https://github.com/mahulchak/quickmerge/issues/72*issuecomment-1590746790__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!Psz-wygMl3AGFdhw0Lv6ZlFnJf7ISs9fblQoPsvUEpkL93DrA3XHMYYW-JmIUJr01vrqGNSWaSv0P6xVLBD_Z-bv$&gt;, &gt; or unsubscribe &gt; <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABZQH2FBRNRMGOY2F2S3U6LXLF2OHANCNFSM6AAAAAAWWHGYM4__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Psz-wygMl3AGFdhw0Lv6ZlFnJf7ISs9fblQoPsvUEpkL93DrA3XHMYYW-JmIUJr01vrqGNSWaSv0P6xVLGmAuFBf$&gt; &gt; . &gt; You are receiving this because you are subscribed to this thread.Message &gt; ID: ***@***.***&gt; &gt; — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;

[ziweiwuzw]

Can you please post your command?
…
On Wed, Jun 14, 2023, 03:42 Wu Ziwei @.> wrote: Hello, I meet same issue, are you figure out? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/https://github.com/mahulchak/quickmerge/issues/72*issuecomment-1590746790;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!Psz-wygMl3AGFdhw0Lv6ZlFnJf7ISs9fblQoPsvUEpkL93DrA3XHMYYW-JmIUJr01vrqGNSWaSv0P6xVLBD_Z-bv$>, or unsubscribe <https://urldefense.com/v3/https://github.com/notifications/unsubscribe-auth/ABZQH2FBRNRMGOY2F2S3U6LXLF2OHANCNFSM6AAAAAAWWHGYM4;!!CzAuKJ42GuquVTTmVmPViYEvSg!Psz-wygMl3AGFdhw0Lv6ZlFnJf7ISs9fblQoPsvUEpkL93DrA3XHMYYW-JmIUJr01vrqGNSWaSv0P6xVLGmAuFBf$> . You are receiving this because you are subscribed to this thread.Message ID: @.>

Sure! Here is the command I'd like to share:
#!/bin/bash
#SBATCH -c 2
source ~/anaconda3/bin/activate ~/anaconda3/envs/genome
PPN=2
genome_file1=/public1/home/genome/nextdenovo/03.ctg_graph/nd.asm.fasta
genome_file2=/public1/home/polish_genome/genome.nextpolish.fasta
output_file=next+flye
nucmer -l 100 -prefix ${output_file} ${genome_file2} ${genome_file1}
delta-filter -r -q -l 10000 ${output_file}.delta > ${output_file}.rq.delta
quickmerge -d ${output_file}.rq.delta -q ${genome_file1} -r ${genome_file2} -hco 5.0 -c 7.0 -l n -ml m -p ${output_file}
Thanks for your help!