User: Campbell.1933

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Posts by Campbell.1933

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Answer: A: Rsubread stopping half-way through align
... thanks.   ...
written 15 months ago by Campbell.19330
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Answer: A: Rsubread stopping half-way through align
... But, one final question - which version of R were you using? tx ...
written 15 months ago by Campbell.19330
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Comment: C: Rsubread stopping half-way through align
... ok - thanks - yes it sounds like a system admin issue   ...
written 15 months ago by Campbell.19330
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Answer: A: Rsubread stopping half-way through align
... So, to date, we've been doing as a fisbatch job and then tried modifying the memory allocation fisbatch --nodes=1 --ntasks-per-node=16 --constraint=CPU-E5-2660 But still seem to be running into the same issue.   I'm guessing fisbatch won't work always (because of memory allocation issue) and so i ...
written 15 months ago by Campbell.19330
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Answer: A: Rsubread stopping half-way through align
... ok  yes, we think it's something to do with disk space too!  Ok, i'll get session info ...
written 15 months ago by Campbell.19330
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Answer: A: Rsubread stopping half-way through align
... Hi - did you get the link to share the folder through google drive?   ...
written 15 months ago by Campbell.19330
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Answer: A: Rsubread stopping half-way through align
... send you a link to a google drive folder with two fastq files in it. One worked and one didn't. There's also a txt file of the readout from Rsubread for both files.   ...
written 15 months ago by Campbell.19330
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Answer: A: Rsubread stopping half-way through align
...   We mapped to Hg19 What's the best way to share a fastq file with you? ...
written 16 months ago by Campbell.19330
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Comment: C: Rsubread stopping half-way through align
... Yes, that was our thought too, but the non-concatentated file also failed   ...
written 16 months ago by Campbell.19330
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Comment: A: Rsubread stopping half-way through align
... The samples divided and run on Hiseq2500 v3 chemistry, high output flowcell, 100SE. The FASTQ files were then catenated. R version 3.3.0 (2016-05-03) -- "Supposedly Educational" being run on a computer cluster. In Rsubread >align(index="reference_index", minFragLength=35, nthreads=30, readfile ...
written 16 months ago by Campbell.19330

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