Comments (5)
ziweiwuzw
commented on September 28, 2024
Hello, I meet same issue, are you figure out?
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mahulchak
commented on September 28, 2024
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?
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chenzhaozhu
commented on September 28, 2024
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 Ziwei ***@***.***>;
发送时间：2023年6月14日(星期三) 下午4:42
收件人："mahulchak/quickmerge" ***@***.***>;
抄送："朱晨朝 ***@***.***>;"Author ***@***.***>;
主题：Re: [mahulchak/quickmerge] Aborted (core dumped) quickmerge (Issue #72)
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Hello, I meet same issue, are you figure out?
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chenzhaozhu
commented on September 28, 2024
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 Chakraborty ***@***.***>;
发送时间：2023年6月15日(星期四) 上午6:30
收件人："mahulchak/quickmerge" ***@***.***>;
抄送："朱晨朝 ***@***.***>;"Author ***@***.***>;
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 ***@***.***> wrote:
> Hello, I meet same issue, are you figure out?
>
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ziweiwuzw
commented on September 28, 2024
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!
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