Comments (8)
There is an error where it is doing the decontamination but losing the resulting files. Tracking the bug and updating the scripts now.
from hannigan_crcvirome_mbio_2018.
I confirmed it is now working as one file at a time, so I am restarting it to run it in parallel.
Fingers crossed!
from hannigan_crcvirome_mbio_2018.
Okay looks like it is running in parallel just fine.
from hannigan_crcvirome_mbio_2018.
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
from hannigan_crcvirome_mbio_2018.
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.
from hannigan_crcvirome_mbio_2018.
Okay I requested 8 axiom cores and I am going to limit make to 8 as well. Lets hope this works.
from hannigan_crcvirome_mbio_2018.
Okay this is running very well. I think it is clear now that the memory was definitely the issue.
from hannigan_crcvirome_mbio_2018.
Done! Moving on.
from hannigan_crcvirome_mbio_2018.
Related Issues (20)
- Create predictive model using 16S Zackular data. HOT 2
- Cluster ORFs into OPFs HOT 2
- Calculate OPF abundance per sample. HOT 4
- Add information for sequencing depth of each of the samples. HOT 2
- Beta diversity between cancer states. HOT 2
- Add python module to CONCOCT. HOT 1
- Fix bacteria IDs to be same as sample IDs. HOT 1
- Rerun contig abundance with both virome and whole meta genome. HOT 2
- Rerun contig clustering with whole meta genome samples as well as virome. HOT 2
- Fix contig fasta problem with wrapped sequence ids. HOT 2
- Rerun files impacted by contig cat error. HOT 3
- Abundance length correction. HOT 2
- Benchmark n50, contig length distribution, alignment rate. HOT 4
- Classify contigs by blasting only the longest reads (rep sequences). Avoid short because they are less informative. HOT 5
- Fix rarefaction of samples going into random forest HOT 2
- Evaluate impact of sequencing depth on model performance. HOT 4
- Plot changes in degree centrality of fusobacterium OTU over time. HOT 1
- Create plot of lysogenic states over cancer progression. HOT 1
- Change repo name HOT 1
- Confirm that use of BLAST's `-max_target_seqs` is intentional HOT 1
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