Check: command not found at step 16 and Died at ......./SqueezeMeta.pl line 811

[Yliub]

Hi, Powerful tool for metagenomic data

I am using the tool for metagenomic analysis, but it always reports an error at STEP 16 as shown in the picture

How can I fix it?

[jtamames]

Hello Run test_install.pl to be sure all is properly installed. Also sens us the syslog file Best, J

[Yliub]

Here is the test_install.pl result and syslog syslog.txt Best, Ba

[jtamames]

Ok, this is a bug on my side. Edit the file 16.addtax2.pl if thescripts directory of the corresponding conda environment (you can use conda info --envs to know where your SqueezeMeta is installed). Change lines 252 and 255, from:

    my $command="checkm tree $bindir $tempdir -t $numthreads -x $thisbin  >> $syslogfile 2>&1";
    # print "**$command**\n";
    system($command);
    my $command="checkm tree_qa $tempdir --tab_table -f $tempout  >> $syslogfile 2>&1";

to

    my $command="$checkm_soft tree $bindir $tempdir -t $numthreads -x $thisbin  >> $syslogfile 2>&1";
    # print "**$command**\n";
    system($command);
    my $command="$checkm_soft tree_qa $tempdir --tab_table -f $tempout  >> $syslogfile 2>&1";

Also, in line 25, where it reads:

our($installpath,

change it for

our($installpath,$checkm_soft

leaving the rest of the line as it is.

Tell me if it works Best, J

[Yliub]

Hello, I change the code as you mentioned,

but it doesn't seems to be working, still report a bug as follows:

[Yliub]

Line 25 was also changed as requested

[jtamames]

Please send us the syslog file, a couple of lines from your terminal is not sufficient to know what is going on

[Yliub]

Hi there， Here is the syslog file, syslog (2).txt

I skipped steps 16 and 17, and ran Step 18, the following steps seemed to be working.

[jtamames]

Ok, notice that you typed "checkm_soft" instead of "$checkm_soft"

[Yliub]

Sorry for the mistakes, I correct it and run --restart again, it reports:

Can't find /home/bio508/NewDisk/liu/metagenomic/4provinces/intermediate/17.4provinces.checkM Stopping in STEP18 -> 17.checkM_batch.pl

[jtamames]

Run restart with -step 16 and --force_overwrite

[Yliub]

Yes, it works, thank you very much for help.

[jtamames]

Welcome! Closing issue