These are chat archives for cboursnell/transfuse

Jul 2016
Jul 01 2016 00:16
Hi Folks: I've been trying to run transrate and transfuse, got all the software installed properly, and ran successfully on one pair of fastq files (one R1 and one R2). Then I try to run on ALL the project data (27 samples, 3 lanes of HiSeq). It creates a bam file of snap alignments to my 1.2M contig(!) Trinity assembly. That bam is 200-265G (depending on whether I'm just running transrate or running it within transfuse. At that point, nothing more is written to the bam file, but "snap-aligner" is still running, using 100-200G RAM (on a 512G RAM machine). Last time, I left it "running" for four days and nothing more was written so I killed the job. I tried to examine the bam file to see if it seemed complete, but it's name-sorted, so I can't run samtools index, flagstat, etc. I would have to coordinate-sort it first! I'm wondering if the job is stalled in a sort step or something? Presuming that the bam is complete, could I stop the job and pick it up with the next command? (And, if so, where do I find the following commands?) I also posted this same message on the transrate board. Thanks!
Richard Smith-Unna
Jul 01 2016 17:09
@monicabritton hmm sorry about that
you should be able to run bamtools on it?