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Using the ecoli dataset, I can't move beyond the map precompute step (i.e., I'm asked to repeat the same qsub command).
Please see the output below. Any suggestions welcomed!
```
[loum@rpbuw218 tes…
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Can NxTrim output fastq file(without gzip) when the input is a fastq.gz file?
If the following process access the fastq file(without gzip), it will become faster.
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When parsing part of the CommonCrawl corpus (which consists of ~1G WARC files where each _record_ is individually compressed), flate2 will return EOF after the first chunk has been decompressed rather…
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There are only 2 undetermined_indices.fastq files in the 2bRAD_Dec15 folder. There should be 5 total- one for each lane sequenced. I suspect the issue is that these files have uniformative names regar…
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instrument IDs to be fixed on :
HCC1954.normal_S22_L001_R1_001.fastq.gz
HCC1954.normal_S22_L001_R2_001.fastq.gz
HCC1954.tumor2_S24_L002_R1_001.fastq.gz
HCC1954.tumor2_S24_L002_R2_001.fastq.gz
HCC1954.…
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Bcbio currently tries to do parallel bgzip by using the pbgzip binary and running grabix afterwards for the index. However, the vanilla bgzip version that is installed by bcbio (bgzip 1.3) now also se…
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Dear Sir,
I just started to use CANU and wanted to analyze Human Genome PacBio data.
So I used the scripts step by step as following:
correcting..
`./canu useGrid=true gridEngine="pbs" gridOption…
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I'm still not sure if it's just taking a long time, but these fastq files I am using are _not_ bgzipped. I think it's just https://github.com/arq5x/grabix/issues/17 instead (fixed, but no release with…
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bamsurgeon stopped running and I got the following error message:
ERROR 2016-04-13 00:48:07.825074 encountered error in mutation spikein: ['5_104998603_104998603_0.444444444444_None']
Traceback (m…
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When run locally Canu fails in the mhap precompute stage with 1 finished job and 4 to compute.
The same data was used on the same machine in canu v1.0 to produce assemblies 1 to 7 without any problem…