User: benv

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benv330
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330
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Canada
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2 years, 2 months ago
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Posts by benv

<prev • 51 results • page 1 of 6 • next >
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Answer: A: abyss-pe without openmpi
... Hi Vinay, Sorry! Yesterday (in another thread) I suggested adding `np=1` to your `abyss-pe` command. But looking at `abyss-pe` script, I see that won't work for running ABySS without MPI. `abyss-pe` tries to detect the number of cores available based on the environment variables set by your job s ...
written 6 days ago by benv330
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Answer: A: ABySS error: sequence and quality must be the same length near ...
... FASTQ records consist of 4 lines each. The first line is the header and contains the read ID. The second line contains the sequence. The third line is just a "+". The fourth line is the quality score string. Each character in the quality score string encodes quality score for the corresponding ...
written 10 days ago by benv330
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Comment: C: installing ABYSS using cygwin
... Fair enough. I will need you to provide some more detailed information before I can help, though. At what step did the commands fail? What was the error message? Was there partial output from the failed command? ...
written 6 months ago by benv330
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... Hmm. I can barely read it but those symlinks look a bit funny. Normally they would be relative symlinks that point directly to the files in the assembly directory, whereas your symlinks are absolute paths that have some funny-looking spaces in them. What O/S are you running this on? Are you tryi ...
written 6 months ago by benv330
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Answer: A: installing ABYSS using cygwin
... I wouldn't recommend trying to run ABySS on cygwin -- I've never tested it and it's not a platform that we officially support. You will have far less problems on Linux/Mac, and I think you will find the story is the same for the majority of bioinformatics software. If you are really set on using ...
written 6 months ago by benv330
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... I'm not sure. What do you see when you do `ls -l` in the assembly directory? ...
written 6 months ago by benv330
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... Oh, I just realized: You are probably seeing the -unitigs/-contigs/-scaffolds.fa files as empty because they are symlinks to the -3.fa,-6.fa,-8.fa files. Btw, the results on the test data set may be worse in 2.0.0 vs. 1.9.0 because I changed some of the default parameter values, in preference of la ...
written 6 months ago by benv330
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Comment: C: abyss-pe 2.0.0 unitig.fa, contig.fa and scaffolds.fa files empty
... Hi @pepijn.kooij, That's odd. It's hard to say what went wrong without some more information. Could you post the ABySS log output here (or in a github gist, if you prefer)? Preferably with verbose logging turned on (add `v=-v` to your `abyss-pe` command). ...
written 6 months ago by benv330
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Comment: C: Issues assembling using ABySS on HTC
... Hi @kingcohn, Glad to hear. No need to concatenate FASTQs prior to running `abyss-pe`. You can specify more than two FASTQs files per paired-end library (preferably ordered like: read1a.fq.gz read2a.fq.gz read1b.fq.gz read2b.fq.gz) or multiple paired-end libraries, if the two pairs of FASTQs have ...
written 6 months ago by benv330
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Comment: C: Issues assembling using ABySS on HTC
... Hi Zachary, Are you compiling from the git repository or from the source tarball? I would recommend using the source tarball, because in that case you won't require autoconf/automake. (If you are compiling from the git repository, you need autoconf and automake installed and you also need to run ` ...
written 6 months ago by benv330

Latest awards to benv

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 12 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 14 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 15 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 16 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 16 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 17 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 24 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS

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