Fastqc works in terminal fastqc not found during jupyter call

Question

[bz3]

I am using Ubuntu 18.04 LTS and fastQC v0.11.8. Using the terminal fastqc is easly called, producing report, graphs and all needed files. In jupyter notebook I tried calling in 2 different ways with two outcomes:

!/usr/local/bin/fastqc /home/bz/Desktop/1coding/pipeline/frag_2.fastq /home/bz/Desktop/1coding/pipeline/frag_1.fastq --extract

i get error

/bin/sh: 1: /usr/local/bin/fastqc: not found

However link to the file is present at this location.

When I give direct path to the file.

!/home/bz/FastQC/fastqc /home/bz/Desktop/1coding/pipeline/frag_2.fastq /home/bz/Desktop/1coding/pipeline/frag_1.fastq --extract

The error:

Can't locate FindBin.pm in @INC (you may need to install the FindBin module)
 (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1
 /usr/local/share/perl/5.26.1 
/usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 
/usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /home/bz/FastQC/fastqc line 4.
BEGIN failed--compilation aborted at /home/bz/FastQC/fastqc line 4.

I checked if the package is installed and it is:perl -e FindBin.pm doesn't throw any errors

Any tips what might be wrong and how can i make fastqc run as a part of python script, many thanks.

[steve]

It is not clear to me how exactly you are executing these commands. Are you using subprocess from Python? In your terminal you should check where FastQC is installed, using a command like which fastqc, then check to make sure that this location is in the PATH when Python/Jupyter/etc are trying to run the command. Or just give the full path to the FastQC binary in your command. The Perl module issues also sound like a PATH problem.

[bz3]

I tried using both subprocess.call() and ! sign,part of jupyter notebook magic to run shell command, with the same error. Fastqc is actually added to the PATH as well as Perl.

which perl 
/usr/bin/perl
which fastqc
/usr/local/bin/fastqc
echo $PATH
/home/bz/anaconda3/bin:/home/bz/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/bin/fastqc