I know emirge has only been tested on versions 0.12* or so of bowtie. But, we had no issues running it up to version 1.1.2 of bowtie. A recent upgrade to bowtie 1.2, however, broke emirge.
The command generated at do_initial_mapping does not seem to work. We get an error saying the file does not appear to be a FASTQ file.
Running latest build of emirge (0.61.0), python 2.7.13, and latest versions of numpy, scipy, biopython, and pysam.
cjfields
commented
6 years ago
Hello.
I know
emirgehas only been tested on versions 0.12* or so ofbowtie. But, we had no issues running it up to version 1.1.2 ofbowtie. A recent upgrade tobowtie 1.2, however, brokeemirge.The command generated at
do_initial_mappingdoes not seem to work. We get an error saying the file does not appear to be a FASTQ file.Running latest build of emirge (0.61.0), python 2.7.13, and latest versions of numpy, scipy, biopython, and pysam.