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TimoLassmann / kalign

A fast multiple sequence alignment program.
GNU General Public License v3.0
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using muti-thread #23

Closed GGanakin closed 4 years ago

GGanakin commented 4 years ago

Hi，i have a large data to align ，Can i use kalign in muti-thread to do it faster

TimoLassmann commented 4 years ago

This is not implemented yet but I am considering it. Can I ask - how large is your data? How many sequences and what is their average length?

GGanakin commented 4 years ago

the data is about 525Mb , total 1265098 sequences. there is anther question now; when i run kalign as follow

kalign -i /data/project/02_OTU/otus.fa -o /data/project/02_OTU/backup/otus.afa

it is alright; but when i run kalign as follow

project="/data/project/" kalign -i ${project}/02_OTU/otus.fa -o ${project}/02_OTU/backup/otus.afa

something is error as

[2020-09-15 17:19:49] : LOG : /home/users/bin/kalign-3.2.3/src/kalign -i /data/project/02_OTU/otus.fa -o /data/project/02_OTU/backup/otus.afa [2020-09-15 17:19:49] : ERROR : Input alignment format could not be detected. (rwalign.c line 314) [2020-09-15 17:19:49] : ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187) [2020-09-15 17:19:49] : ERROR : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383) [2020-09-15 17:19:49] : ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353)

can you help me ? thank you

发件人: TimoLassmann notifications@github.com 发送时间: 2020年9月15日 3:50 收件人: TimoLassmann/kalign kalign@noreply.github.com 抄送: yxhmjl maojunlai8@outlook.com; Author author@noreply.github.com 主题: Re: [TimoLassmann/kalign] using muti-thread (#23)

This is not implemented yet but I am considering it. Can I ask - how large is your data? How many sequences and what is their average length?

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TimoLassmann commented 4 years ago

Version 3.3 now has multi-threading support. Unfortunately, I am unable to replicate the error above.