User: Lina F

gravatar for Lina F
Lina F160
Reputation:
160
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Trusted
Location:
Boston, MA
Last seen:
6 months, 2 weeks ago
Joined:
5 years, 3 months ago
Email:
l**********@gmail.com

Posts by Lina F

<prev • 92 results • page 1 of 10 • next >
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Comment: 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 F160
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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 F160
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SPAdes error code -6
... 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: ...
assembly metagenomics spades written 6 months ago by Lina F160
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Comment: C: How does bbduk calculate it's memory requirements?
... 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 F160
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Comment: C: How does bbduk calculate it's memory requirements?
... 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 F160
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How does bbduk calculate it's memory requirements?
... 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= ...
bbduk docker memory written 8 months ago by Lina F160
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Comment: C: Ran dipSpades for a diploid fungus genome -- now what?
... 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 F160
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Comment: C: Error building snpEff database "Transcript 'hypothetical_protein' already exist
... 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 F160
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Comment: C: Error building snpEff database "Transcript 'hypothetical_protein' already exist
... it's GCA_001007165.2 ...
written 18 months ago by Lina F160
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Error building snpEff database "Transcript 'hypothetical_protein' already exists"
... 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 ...
database snpeff build written 18 months ago by Lina F160 • updated 18 months ago by Pierre Lindenbaum125k

Latest awards to Lina F

Popular Question 8 months ago, created a question with more than 1,000 views. For SPAdes is running out of memory
Supporter 8 months ago, voted at least 25 times.
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