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humann3多线程求助 #11

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tutu256 opened this issue Jul 16, 2024 · 0 comments
Open

humann3多线程求助 #11

tutu256 opened this issue Jul 16, 2024 · 0 comments

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@tutu256
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tutu256 commented Jul 16, 2024

您好,在运行单样本使用humann3时可以正常运行,使用rush多任务时报错,请问如何解决

如果服务器性能好,请设置--threads值为8/16/32

tail -n+2 result/metadata.txt | cut -f1 | rush -j 2
"humann --input temp/concat/{1}.fq
--output temp/humann3/ --threads 3 --metaphlan-options '--bowtie2db /db/metaphlan4 --index mpa_vOct22_CHOCOPhlAnSGB_202212 --offline'"
报错如下:
(humann3) xumingyuan@cn5:meta$tail -n+2 result/metadata.txt|cut -f1|rush -j 2 \

"humann --input temp/concat/${i}.fq --output temp/humann3/ --threads 32 -- metaphlan-options '--bowtie2db /home/xumingyuan/data_HD/database/metaphlan4 --index mpa_vOct22_CHOCOPhlAnSGB_202212 --offline'"
/bin/bash: line 1: humann: command not found
/bin/bash: line 1: humann: command not found
[ERRO]
我修改补全了humann3的地址,tail -n+2 result/metadata.txt|cut -f1|rush -j 2
"/home/xumingyuan/data_HD/micromamba/envs/humann3/bin/humann --input temp/concat/${i}.fq --output temp/humann3/ --threads 32 -- metaphlan-options '--bowtie2db /home/xumingyuan/data_HD/database/metaphlan4 --index mpa_vOct22_CHOCOPhlAnSGB_202212 --offline'"
humann: error: unrecognized arguments: -- metaphlan-options --bowtie2db /home/xumingyuan/data_HD/database/metaphlan4 --index mpa_vOct22_CHOCOPhlAnSGB_202212 --offline
[ERRO] 。
非常感谢。

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