Step 14 - SqueezeMeta_conf.pl not found

[danfrks]

Hello,

I have an issue where SM does not run the binning algorithms because it does not find the config file. I am sure it is something simple I am missing, thank you in advance for taking a look.

(SqueezeMeta) danielfarkas@urlws00002:~/Metagenomics/Atrazine/raw_data/Atrazine$ sudo perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl /home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine/ -step 14
[0 seconds]: STEP14 -> BINNING: 14.runbinning.pl
  Running maxbin from /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl
Can't find SqueezeMeta_conf.pl in Atrazine. Is the project path ok? at /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl line 15.
ERROR in STEP14 -> /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl
wc: /home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine/intermediate/binners/maxbin/: Is a directory
WARNING in STEP14 -> /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl. No maxbin results!

The conf.pl file is indeed in the project folder.

`$version = "1.4.0, May 2021";
$mode = "seqmerge";
$date = "Mon May  9 11:47:12 2022";

$installpath = "/home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta";
#-- Project dir (calculated dinamically on execution, DO NOT MODIFY)

use File::Basename;
use Cwd 'abs_path';
$projectdir   = abs_path(dirname(__FILE__));

Best,

Daniel

[fpusan]

Why are you running this with sudo? Not 100% what is happening but I can imagine how this could lead to problems.

[danfrks]

The error was displayed without the sudo command as well. I was thinking it is a perl issue with calling the ARVG variable and I tried with sudo. I have no experience with perl and limited experience with bash/Linux in general, and I was trying to figure out what's going on before opening a thread. The result is the same with and without sudo anyway. The program was running from step 7 to 13 with no problems before the error in step 14,which makes it more baffling.

[fpusan]

Assuming the SqueezeMeta_conf.pl file is in /home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine

Try

cd ~/Metagenomics/Atrazine/raw_data/Atrazine$ sudo perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl /home/danielfarkas/Metagenomics/Atrazine/raw_data/

perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl Atrazine -step 14

[danfrks]

I have tried to run from within the directory of the project, and from the home directory. Same error both times.

However, it asks me if I want to remove the log file; either way (y or n), the error persists.

SqueezeMeta) danielfarkas@urlws00002:~/Metagenomics/Atrazine/raw_data/Atrazine$ perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl /home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine -step 14
rm: remove write-protected regular file '/home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine/temp/Atrazine.log'? y
[1 seconds]: STEP14 -> BINNING: 14.runbinning.pl
  Running maxbin from /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl
Can't find SqueezeMeta_conf.pl in Atrazine. Is the project path ok? at /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl line 15.
ERROR in STEP14 -> /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl
wc: /home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine/intermediate/binners/maxbin/: Is a directory
WARNING in STEP14 -> /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/bin_maxbin.pl. No maxbin results!

config_and_syslog.zip

[fpusan]

By looking at the syslog file it seems that the program died several times, but it shouldn't be a problem per se...

Can you try running the latest version of SqueezeMeta (without sudo) on the test data we provide when downloading the databases? Let's see if the issue persists.

[jtamames]

Hello As @fpusan says, what you need to do is to cd to the parent directory of your project (/home/danielfarkas/Metagenomics) and invoke restart.pl using the project name:

perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl Atrazine -step 14

or, altenatively, use the project path from any location:

perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl /home/danielfarkas/Metagenomics/Atrazine -step 14

You did instead:

perl /home/danielfarkas/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/restart.pl /home/danielfarkas/Metagenomics/Atrazine/raw_data/Atrazine -step 14

Notice the difference, you are not providing a project name or a project path. A quick reading of the manual can help to solve issues like this. Best, J

[danfrks]

Solved. The correct directory was ~/Metagenomics/Atrazine/raw_data.

Thank you and sorry for bothering you with this.