User: pepijn.kooij

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Posts by pepijn.kooij

<prev • 12 results • page 1 of 2 • next >
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... For privacy reasons I blacked out those parts. I'm running it on Linux Ubuntu 14.04 with Biolinux 8. The symlinks look correct, but still my files appear empty. Might it be in the permission of the files? I'm very puzzled by why this is. Previously, with 1.9.0, and with other assemblers that create ...
written 12 months ago by pepijn.kooij0
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... Yes, for privacy reasons I blacked out those parts. I'm running it on Linux Ubuntu 14.04 with Biolinux 8. The symlinks look correct, but still my files appear empty. Might it be in the permission of the files? I'm very puzzled by why this is. Previously, with 1.9.0, and with other assemblers that cr ...
written 12 months ago by pepijn.kooij0
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... It seems to look ok, which makes it even weirder... ![ls -l of my output folder][1] [1]: http://pwkooij.com/files_to_share/abyss-pe_20160906.png ...
written 12 months ago by pepijn.kooij0
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... I was thinking that it would be something like that, this is different from 1.9.0, am I right? However, there's still a problem. With other assemblers I have similar symlink files, and using $nano file, I get to see the sequences. When I try that with the ones generated by abyss 2.0.0, it just simp ...
written 12 months ago by pepijn.kooij0
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... The verbose is too long to post here, so I deposited on my github: [abyss-2.0.0_test_verbose.log][1] [1]: https://github.com/pwkooij/genome-scripts/blob/master/abyss-2.0.0_test_verbose.log ...
written 12 months ago by pepijn.kooij0
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... Yes, more than enough. I actually tried my own data first, with two separate datasets, which I ran through a bash script. Aside from the fact I know there is more than enough space (over 400Gb free), the total amount written for for the second set is larger than the expected size for the three files ...
written 12 months ago by pepijn.kooij0
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abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... I just deployed abyss 2.0.0 and tried to run the abyss-pe pipeline, using both my own data as well as the provided test data, but the resulting unitig.fa, contig.fa and scaffolds.fa files are empty. The verbose does give statistics for these files, so I'm a bit puzzled as to why these files are empt ...
assembly abyss-pe abyss written 12 months ago by pepijn.kooij0 • updated 10 months ago by phair.nikki0
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Comment: C: abyss-pe reading files endlessly with se command added
... Thanks, I'll try to add those export open-mpi lines to my script to see if that helps with larger maxk values and will post the results here. ...
written 18 months ago by pepijn.kooij0
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Answer: A: abyss-pe reading files endlessly with se command added
... Ok, I figured what was happening, but still confused. I previously had abyss deployed with a maxk set at 256, redeploying it with maxk set at 96 did the trick. The strange thing is that the abyss github readme.md says this: > The default maximum k-mer size is 64 and may be decreased to reduce m ...
written 18 months ago by pepijn.kooij0
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Comment: C: abyss-pe reading files endlessly with se command added
... Yes, I read that, but it's not even getting to that point. It just 'hangs' at reading in the files. I had one analysis turned on on Friday, and it was still reading the files this morning (Monday). I killed the process to play around with the settings and try to figure out what the issue is, without ...
written 18 months ago by pepijn.kooij0

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