Run human decontamination (deconseq)

[Microbiology]

There is an error where it is doing the decontamination but losing the resulting files. Tracking the bug and updating the scripts now.

[Microbiology]

I confirmed it is now working as one file at a time, so I am restarting it to run it in parallel.

Fingers crossed!

[Microbiology]

Okay looks like it is running in parallel just fine.

[Microbiology]

Okay Im getting about half of the samples to complete. The others are giving me this error:

[bsw2_aln] read 81045 sequences (10000086 bp)...
[bsw2_aln] read 80551 sequences (10000112 bp)...
[bsw2_aln] read 80275 sequences (10000025 bp)...
[bsw2_aln] read 80311 sequences (10000090 bp)...
cp: cannot stat `data/QC/MG100065_R2.fastq.output/*clean.fq': No such file or directory
cp: cannot stat `data/QC/MG100065_R2.fastq.output/*cont.fq': No such file or directory
make: *** [data/HumanDecon/MG100065_R2.fastq] Error 1
ERROR: system call "/mnt/EXT/Schloss-data/bin/deconseq-standalone-0.4.3/bwa64 bwasw -A -f data/QC/MG100097_R2.fastq.output/1477433425_hsref_hs_ref_GRCh38_p2.tsv /mnt/EXT/Schloss-data/bin/deconseq-standalone-0.4.3/db/hs
_ref_GRCh38_p2 data/QC/MG100097_R2.fastq" failed: 139.

Try 'deconseq -h' for more information.
Exit program.

The directories sit with empty reference files...

MG100119_R2.fastq.output:
total 4.0K
-rw-r--r--. 1 ghannig schlosslab 0 Oct 25 18:05 1477433099_hsref_hs_ref_GRCh38_p2.tsv
-rw-r--r--. 1 ghannig schlosslab 0 Oct 25 18:04 1477433099

[Microbiology]

Okay I looked more into this and the 139 exit code has to do with a segmentation fault (memory violation). Surprise surprise. So I need to make sure I am more conservative with my memory usage the next time I run it.

[Microbiology]

Okay I requested 8 axiom cores and I am going to limit make to 8 as well. Lets hope this works.

[Microbiology]

Okay this is running very well. I think it is clear now that the memory was definitely the issue.

[Microbiology]

Done! Moving on.