Check properly the return code of system calls for sub-scripts

[loic-couderc]

Describe the bug The script sga_assemble.py uses subprocess.call without checking the return code. By consequence, MATAM will continue its execution until an another error occur.

• [x] sga_assemble.py

To Reproduce Run matam with default parameter and use a Phred+64 fastq file.

Expected behavior Stop MATAM as soon as possible when a system call return a non zero code.

The following scripts may be impacted by a similar problem:

• [x] index_default_ssu_rrna_db.py (the rc is not set at the end of the script)
• [x] scripts/evaluate_assembly.py
• [x] scripts/index_ref_db.py (the rc is not set at the end of the script)
• [x] scripts/matam_assembly.py

[loic-couderc]

Changing subprocess.call by subprocess.check_call in sga_assemble.py has for consequence to end MATAM prematurely.

# the following command fails because merged_output.fa is empty (6/131 components)
CMD: /home/lcouderc/anaconda3/envs/matam/bin/sga index -d 1000000 -t 1 merged_output.fa

[loic-couderc]

We have to distinguish 2 cases:

• During the filtering step of SGA, no reads are left, we have exit with 0 code. (A WARNING will be logged).
• If any SGA command fails, kill the pool and stop MATAM.