(ERR): bowtie2-align died with signal 13 (PIPE)

[kaeldai]

Tried running SISRS (develop branch) on a FreeBSD machine, using both minia and velvet. Kept receiving the following error:

==== Aligning FILELIST ../SISRS_test_data/T1/T1 ==== [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE null: bowtie2-align died with signal 13 (PIPE) ==== Done Aligning ====

When bowtie finishes the program continues and output for all the bams:

[E::hts_open_format] fail to open file '../SISRS_test_data/T1/T1.bam' samtools index: failed to open "../SISRS_test_data/T1/T1.bam": No such file or directory

[kaeldai]

Ran the command:

./sisrs sites -g 1745690 -p 40 -m 4 -f test_data -t .99 -a minia

data was taken from rachelss/SISRS_test_data

[rachelss]

The latest version of bowtie2 requires specifying the output file with a flag. I updated the SISRS script and it should work now.