User: Lina F
Lina F • 160
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- Boston, MA
- Last seen:
- 6 months, 2 weeks ago
- Joined:
- 5 years, 3 months ago
- Email:
- l**********@gmail.com
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 6 months ago by
Lina F • 160
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Comment:
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 6 months ago by
Lina F • 160
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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 6 months ago by
Lina F • 160
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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 8 months ago by
Lina F • 160
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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 8 months ago by
Lina F • 160
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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 8 months ago by
Lina F • 160
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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 10 months ago by
Lina F • 160
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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 18 months ago by
Lina F • 160
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... it's GCA_001007165.2 ...
written 18 months ago by
Lina F • 160
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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 18 months ago by
Lina F • 160
• updated
18 months ago by
Pierre Lindenbaum ♦ 125k
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