User: shammond
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Posts by shammond
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... As written, the log2 fold-change threshold that you're using in Method B is 0. Try lfcThreshold=1. ...
written 10 months ago by
shammond • 0
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... Hi Rayan/Devon,
I was assembling a set of 2x250 human reads with 72x coverage using the beta version of minia 3 that you kindly provided me, when I encountered this error:
[bug detected in adjacency data structure] was supposed to delete node AAAAAAAAAAAAAAAAAAAAAGGTCTGGGGTGTCATTATATTGCCCAGGCT ...
written 3.8 years ago by
shammond • 0
• updated
3.8 years ago by
Rayan Chikhi • 1.4k
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Comment:
C: Run ABYSS for single-ended reads
... Hi Kate,
Those abyss-fac results mean that all of the contigs were shorter than 500 bp, and since its default behaviour is to report the stats on contigs >= 500, all the other stats are 0. You can change this length cut-off with the -t option.
Even without pairing information, you should be able ...
written 3.8 years ago by
shammond • 0
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... Hi guys,
Using "-debloom original" with the binary you provided did the trick. And I'll check out those analysis tools. Thanks for your help!
Austin ...
written 3.8 years ago by
shammond • 0
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... Hi, the contigs were a bit shorter than I was hoping for. My N50 was about 3kb. I tried several k up to 128, where my N50 reached 4.2kb. k larger than 128 failed with this error:
[DSK: nb solid kmers found : 3242850977 ] 101 % elapsed: 746 min 28 sec remaining: 0 min 0 sec cpu: 238. ...
written 3.9 years ago by
shammond • 0
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... When I set max-memory to 0 and min-abundance to "auto", minia reports peak memory of 24.9 GB. ...
written 3.9 years ago by
shammond • 0
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... Hi Rayan, I have one set of PET reads, so two gzipped read files, 59 GB and 63 GB. Minia 3 reports 3045237911 solid kmers.
Full output stats from the run:
-in : hsapiens-files.txt
-abundance-min : 4
-kmer-size ...
written 3.9 years ago by
shammond • 0
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... Thanks for that beta, Rayan. It was able to assemble my data at k64, and reported max memory usage of 872 GB. Are there any parameters I could tweak in 2.0.3 to get around this memory issue? ...
written 3.9 years ago by
shammond • 0
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... Hi, I've tried values up to 2200000 for -max-memory, and at the top end I will get an error like this:
[DSK: Pass 1/1, Step 2: counting kmers ] 50.3 % elapsed: 116 min 11 sec estimated remaining: 114 min 34 sec cpu: 408.0 % mem: [308387, 308436, 308436] MB Warning: forced to allocat ...
written 3.9 years ago by
shammond • 0
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... Hi guys,
I'm having some problems assembling a 2 x 250 bp, 76x coverage data set using Minia 2.0.3:
[DSK: Collecting stats on read sample ] 100 % elapsed: 5 min 59 sec estimated remaining: 0 min 0 sec cpu: 297.9 % mem: [ 844, 844, 844] MB
[DSK: Pass 1/1, Step 2: countin ...
written 3.9 years ago by
shammond • 0
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For Minia crashes during kmer counting
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