Eric Edsinger
Eric Edsinger
Sure! Here is the last one (09 to 36 are like this one - only an sh script in the folder): /scratch2/eedsinger/projects/genomes/zanfona-5x-50x/octopus-sinensis/output/3-nextDenovo-assembly/02.cns_align/02.cns_align.sh.work/cns_align36/nextDenovo.sh #!/bin/bash set -xveo pipefail hostname cd /scratch2/eedsinger/projects/genomes/zanfona-5x-50x/octopus-sinensis/output/3-nextDenovo-assembly/02.cns_align/02.cns_align.sh.work/cns_align36 (...
And here is the first one (01-08 are similar to this): hostname + hostname cd /scratch2/eedsinger/projects/genomes/zanfona-5x-50x/octopus-sinensis/output/3-nextDenovo-assembly/02.cns_align/02.cns_align.sh.work/cns_align01 + cd /scratch2/eedsinger/projects/genomes/zanfona-5x-50x/octopus-sinensis/output/3-nextDenovo-assembly/02.cns_align/02.cns_align.sh.work/cns_align01 ( time /nadata/mnlsc/home/eedsinger/software/nextdenovo/NextDenovo/bin/minimap2-nd -I 6G --step 2 -t 7 -x ava-pb...
Ok! I'll kill things and restart fresh....
Actually - rather than starting totally fresh, I updated the run file and just deleted folders 2 and 3 to save a little time and see how things go with...
minimap2-nd started up - first 8 of 36 jobs again - mid_occ is now under 1000 at 427 - jobs are still running under status S but that might be...
Well - things haven't advanced past the first 8 jobs after several days now. It feels like it might be similar to before... Is there anything you might suggest I...
Good news - I left things running and one of the initial 8 jobs finished after 4 days and a second one after 5 - so two new jobs now...
The remaining 6 jobs of the initial round finished at around 7 days / 1300 CPUs hours per 7-CPU job - so second round of 4-5 rounds is now fully...
Wow - so this is really running long already and still weeks to go. I'm actually trying to improve on a wtdbg2 assembly - do you think NextDenovo is likely...
I'm getting a Salmon error similar to aaronk - I'm running transfuse 0.5.0 with packaged transrate 1.0.1 and packaged salmon 0.4.2. Please see attached file for log. [transfuse-log.txt](https://github.com/cboursnell/transfuse/files/800440/transfuse-log.txt)