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SchlossLab / Hannigan_CRCVirome_mBio_2018

Investigating the gut virus communities associated with colon cancer.
MIT License
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Rerun contig abundance with both virome and whole meta genome. #38

Closed Microbiology closed 7 years ago

Microbiology commented 7 years ago

There seem to be some problems with the alignments for making relative abundance tables.

Microbiology commented 7 years ago

Here are the problems, as far as I can tell.

  1. What is going on with the reference?
bash ./bin/CreateContigRelAbundTable.sh \
                ./data/totalcontigsvirus.fa \
                ./data/virusseqsfastq \
                ./data/ContigRelAbundForGraphVirus.tsv
Getting contig relative abundance table...
Building bowtie reference...
Building a SMALL index
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
  1. Bacterial alignments are running out of memory, so probably need to run these on their own nodes.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /opt/bioinf/bowtie2/2.2.1/bin/bowtie2-align-s --wrapper basic-0 -x ./data/tmpbowtie/bowtieReference/bowtieReference -q -S ./data/bacteriaseqsfastq/MG100154_R2.fastq-bowtie.sa
(ERR): bowtie2-align exited with value 1
Error: Encountered internal Bowtie 2 exception (#1)
Command: /opt/bioinf/bowtie2/2.2.1/bin/bowtie2-align-s --wrapper basic-0 -x ./data/tmpbowtie/bowtieReference/bowtieReference -q -S ./data/bacteriaseqsfastq/MG100130_R2.fastq-bowtie.sa
(ERR): bowtie2-align exited with value 1
Out of memory allocating the ebwt[] array for the Bowtie index.  Please try
again on a computer with more memory.
Out of memory allocating the ebwt[] array for the Bowtie index.  Please try
again on a computer with more memory.
Microbiology commented 7 years ago

Ran across multiple jobs/cores. Problem solved. Moving on.