fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code

[k1sauce]

fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code.

This seems like a problem since the expected output files are all made, but the reported values will be different when the aligner fails. Also it would be nice to have a non-zero exit code when the aligner fails since I am using fastq screen with nextflow, and it does not crash the workflow when it fails.

This is the out put of the log:
See the line:
Aligner warning: Killed
Aligner warning: (ERR): bowtie2-align exited with value 137

+ fastq_screen --aligner bowtie2 seq006983_S23_L004_R2_001.fastq.gz
Using fastq_screen v0.14.0
Reading configuration from '/usr/local/share/fastq-screen-0.14.0-0/fastq_screen.conf'
Adding database Mitochondria
Adding database Arabidopsis
Adding database PhiX
Adding database Rat
Adding database E_coli
Adding database Mycoplasma
Adding database Vectors
Adding database Mouse
Adding database Adapters
Adding database Drosophila
Adding database Worm
Adding database Lambda
Adding database rRNA
Adding database Yeast
Using 1 threads for searches
Option --subset set to 100000 reads
Processing seq006983_S23_L004_R2_001.fastq.gz
Counting sequences in seq006983_S23_L004_R2_001.fastq.gz
Not making subset of 100000 since 24708 actual sequences is too low or close enough
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Mitochondria
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Arabidopsis
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against PhiX
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Rat
Aligner warning: Killed
Aligner warning: (ERR): bowtie2-align exited with value 137
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against E_coli
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Mycoplasma
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Vectors
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Mouse
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Adapters
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Drosophila
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Worm
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Lambda
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against rRNA
Searching seq006983_S23_L004_R2_001.fastq.gz_temp_subset.fastq against Yeast
Processing complete

[StevenWingett]

Thanks for letting me know. I'll look into ways to make FastQ Screen fail more elegantly when necessary. This fix should be incorporated into the next update.