User: Lina F
Lina F • 190
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- Boston, MA
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- 1 year, 3 months ago
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- 6 years ago
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Posts by Lina F
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C: SPAdes error code -6
... At this point, I am ok with just tossing the small sample. One could argue that it probably doesn't add much information anyways.
However, what I didn't expect was that SPAdes would just not assemble anything when given these two libraries (even though sample2 on it's own does assemble into contigs ...
written 15 months ago by
Lina F • 190
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C: SPAdes error code -6
... Thank you for your suggestions!
- I tried assembling just sample1 -- that fails and I assume it's because the sample is too complex and/or doesn't have enough reads for the complexity.
- I tried just assembling sample2 -- that assembles fine
- I tried first concatenating the files of the two sam ...
written 15 months ago by
Lina F • 190
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... Hi all,
I recently ran SPAdes on two samples and encountered an error code of -6.
I noticed that one of the samples I used was big and the other one had much fewer reads. I assume the error could come from the smaller dataset not having enough reads.
Number of FASTQ records in the smaller sample: ...
written 15 months ago by
Lina F • 190
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... I upped the memory to 8 Gb for the docker container and it worked! bbduk used **-Xmx1267m -Xms1267m**
It seems like I underestimated how much memory the kmers take up and maybe the autodetect feature really does work differently in a docker container.
Thanks for helping me debug this!! ...
written 17 months ago by
Lina F • 190
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... It's actually pretty small:
$> ls -lah reference.fa
-rwxrwxrwx 1 1002 1002 115K Oct 14 2016 reference.fa
I thought I could avoid setting Xmx and Xms manually. Maybe that is not the case.
Thanks for any suggestions you might have! ...
written 17 months ago by
Lina F • 190
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... I ran bbduk using:
/opt/bbmap/bbduk.sh in1=R1.fq.gz in2=R2.fq.gz out1=cleaned_R1.fq.gz out2=cleaned_R2.fq.gz ref=reference.fa k=31 hdist=1 stats=stats.txt overwrite=true
Which bbduk translated to:
java -ea -Xmx299m -Xms299m -cp /opt/bbmap/current/ jgi.BBDuk in1=R1.fq.gz in2=R2.fq.gz out1= ...
written 17 months ago by
Lina F • 190
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... Unfortunately, I couldn't figure out what the best thing to do was. None of the advice I found on the internet made me feel confident in dipSpades :-( ...
written 19 months ago by
Lina F • 190
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... Thank you, this worked! However, now it's finding other non-unique names... looks like I will have to run this fix a few times. Thanks! ...
written 2.3 years ago by
Lina F • 190
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... it's GCA_001007165.2 ...
written 2.3 years ago by
Lina F • 190
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... Hi all,
I am trying to build a snpEff database but I'm running into the following error message:
java.lang.RuntimeException: Transcript 'hypothetical_protein' already exists
at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.add(SnpEffPredictorFactory.java:135)
at ...
written 2.3 years ago by
Lina F • 190
• updated
2.3 years ago by
Pierre Lindenbaum ♦ 131k
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