User: Lina F

gravatar for Lina F
Lina F150
Reputation:
150
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Trusted
Location:
Boston, MA
Last seen:
1 week, 4 days ago
Joined:
4 years, 9 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 11 days ago by Lina F150
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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 11 days ago by Lina F150
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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 15 days ago by Lina F150
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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 weeks ago by Lina F150
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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 weeks ago by Lina F150
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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 weeks ago by Lina F150
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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 3 months ago by Lina F150
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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 12 months ago by Lina F150
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Comment: C: Error building snpEff database "Transcript 'hypothetical_protein' already exist
... it's GCA_001007165.2 ...
written 12 months ago by Lina F150
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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 12 months ago by Lina F150 • updated 12 months ago by Pierre Lindenbaum121k

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For SPAdes is running out of memory
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Popular Question 10 months ago, created a question with more than 1,000 views. For SPAdes is running out of memory
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Popular Question 12 months ago, created a question with more than 1,000 views. For SPAdes is running out of memory
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Popular Question 17 months ago, created a question with more than 1,000 views. For How to assemble complex soil metagenome datasets?
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