Vishal Koparde, PhD

icon indicating a website link https://ccbr.ccr.cancer.gov/

icon company NCI icon location Bethesda/Frederick, MD icon location Manager, Bioinformatics [NCI/CCR, CCBR, FNLCR]

Results 7 comments of Vishal Koparde, PhD

finding pseudoalignments for the reads ...Segmentation fault (core dumped)

Any idea if this issue has been resolved yet. I am also getting something very similar: ``` [ bam] writing pseudoalignments to BAM format .. /spin1/swarm/kopardevn/M0tDGHNewa/cmd.10: line 1: 12564 Segmentation...

Failed to open file talon_tmp/interval_files/1_10554_248944156.bam

PR with a [fix](https://github.com/mortazavilab/TALON/pull/75)

Issue commands do not work with non-classic Projects

Any updates? Do commands now work with non-classic Projects?

multiprocessing

I am getting the same error: """ Traceback (most recent call last): File "../scripts/bam2tssscore.v2.py", line 70, in bam_array=bam.array(features = tss_ext,bins = bins,processes = args.ncpu) File "/usr/local/Anaconda/envs/py2.7/lib/python2.7/site-packages/metaseq/_genomic_signal.py", line 122, in array...

multiprocessing

I am still getting the same error... Any solution guys?

"dry run" option?

Is **dry-run** or **plan** feature available in the latest nexflow version?

URL from demo.py is broken

Thanks, @sdomanskyi . I will give this a try.