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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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01.run_assembly.pl (megahit) #751

Closed zhenzhao123 closed 6 months ago

zhenzhao123 commented 7 months ago

Hello, I have a trouble. such as this: my code is :SqueezeMeta.pl -m coassembly -p low_salt -s /home/lmb600/work_space/li/raw_data/yandu/sample2 -f ../yandu/ -t 100 It reply comments: SqueezeMeta v1.2.0 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started Tue Nov 14 14:54:10 2023 in coassembly mode Now creating directories Reading configuration from /home/lmb600/work_space/li/raw_data/yandu/low_salt/SqueezeMeta_conf.pl /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/00.low_salt.samples 1 sample found Now merging files [0 seconds]: STEP1 -> RUNNING CO-ASSEMBLY: 01.run_assembly.pl (megahit) Running assembly with megahit Error running command: /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/raw_fastq/par1.fastq.gz -2 /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/raw_fastq/par2.fastq.gz -t 100 -o /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/megahit >> /home/lmb600/work_space/li/raw_data/yandu/low_salt/syslog 2>&1 at /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/01.run_assembly.pl line 107. Stopping in STEP1 -> 01.run_assembly.pl (megahit) Died at /home/lmb600/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 612. please told me how to resolve,Thanks. best zhao

jtamames commented 7 months ago

Hello It should work, but coassembly is needed when more that one sample is present. In your case, you could specify "sequential" as mode, since you just have one sample. But as it should work anyways, please do the following: ls -ltr /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/raw_fastq/ and please remember to attach the syslog file when you report an issue. Best, J

zhenzhao123 commented 7 months ago

Thanks, however, when I use the 9 samples, it is the same results, such as: SqueezeMeta.pl -m coassembly -p low_salt -s /home/lmb600/work_space/li/raw_data/yandu/sample2 -f ../yandu/ -t 100

SqueezeMeta v1.2.0 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started Tue Nov 14 14:25:59 2023 in coassembly mode Now creating directories Reading configuration from /home/lmb600/work_space/li/raw_data/yandu/low_salt/SqueezeMeta_conf.pl /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/00.low_salt.samples 9 samples found: 9d25ppt2 9d25ppt3 9d30ppt2 9d25ppt1 9d30ppt1 9d20ppt1 9d20ppt3 9d30ppt3 9d20ppt2

Now merging files [33 seconds]: STEP1 -> RUNNING CO-ASSEMBLY: 01.run_assembly.pl (megahit) Running assembly with megahit Error running command: /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/raw_fastq/par1.fastq.gz -2 /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/raw_fastq/par2.fastq.gz -t 100 -o /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/megahit >> /home/lmb600/work_space/li/raw_data/yandu/low_salt/syslog 2>&1 at /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/01.run_assembly.pl line 107. Stopping in STEP1 -> 01.run_assembly.pl (megahit) Died at /home/lmb600/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 612.

jtamames commented 7 months ago

Ups.. I have just realize you are using version 1.2.0. We are no longer supporting that one, because current version is 1.6.3 and there are tons of issues solved since then. Please update your SqueezeMeta to the current version and try again. Best, J

zhenzhao123 commented 7 months ago

OK, thank you J. Please briefly describe how to update the current version and whether the downloaded database needs to be changed. Please give me a suggestion.

------------------ 原始邮件 ------------------ 发件人: "Javier @.>; 发送时间: 2023年11月14日(星期二) 晚上11:55 收件人: @.>; 抄送: "Zhao @.>; @.>; 主题: Re: [jtamames/SqueezeMeta] 01.run_assembly.pl (megahit) (Issue #751)

Ups.. I have just realize you are using version 1.2.0. We are no longer supporting that one, because current version is 1.6.3 and there are tons of issues solved since then. Please update your SqueezeMeta to the current version and try again. Best, J

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

jtamames commented 7 months ago

Please check the manual

zhenzhao123 commented 7 months ago

Thank you!

fpusan commented 6 months ago

Closing due to lack of activity, feel free to reopen