User: shammond

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shammond0
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Posts by shammond

<prev • 9 results • page 1 of 1 • next >
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Minia bug with "--debloom original"
... 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 ...
minia written 9 months ago by shammond0 • updated 8 months ago by Rayan Chikhi1.1k
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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 9 months ago by shammond0
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Comment: C: Minia crashes during kmer counting
... 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 9 months ago by shammond0
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Comment: C: Minia crashes during kmer counting
... 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 10 months ago by shammond0
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Comment: C: Minia crashes during kmer counting
... When I set max-memory to 0 and min-abundance to "auto", minia reports peak memory of 24.9 GB. ...
written 10 months ago by shammond0
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Comment: C: Minia crashes during kmer counting
... 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 10 months ago by shammond0
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Comment: C: Minia crashes during kmer counting
... 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 11 months ago by shammond0
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Comment: C: Minia crashes during kmer counting
... 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 11 months ago by shammond0
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Minia crashes during kmer counting
... 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 ...
minia written 11 months ago by shammond0

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