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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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10.mapsamples.pl #757

Closed zhenzhao123 closed 7 months ago

zhenzhao123 commented 7 months ago

Hello! I got a location error when I ran Squeezemeta, and the feedback is as follows: stat: No such file or directory Warning: Could not open read file "/home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_1" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 An error occurred during mapping with command /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/bin/bowtie2/bowtie2 -x /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/low_salt.bowtie -1 /home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_1 -2 /home/lmb600/work_space/li/raw_data/yandu/low_salt/temp/low_salt.9d20ppt3.current_2.gz --quiet -p 100 -S /home/lmb600/work_space/li/raw_data/yandu/low_salt/data/bam/low_salt.9d20ppt3.sam --very-sensitive-local! at /home/lmb600/anaconda3/envs/SqueezeMeta/SqueezeMeta/scripts/10.mapsamples.pl line 267. Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /home/lmb600/work_space/li/raw_data/yandu/low_salt/syslog file (zip it first) Died at /home/lmb600/anaconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941. This is my syslog file. syslog.gz

jtamames commented 7 months ago

Hello Is this the same issue that you opened yesterday?

zhenzhao123 commented 7 months ago

Yes, I re-ran the Step 10 script as you requested yesterday and found that the problem still exists. Today I re-ran it from scratch and found that the problem still occurs.

jtamames commented 7 months ago

Ok,then please do not open two issues for the same problem