User: Lina F
Lina F • 150
- Reputation:
- 150
- Status:
- 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 >
0
votes
0
answers
108
views
0
answers
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 F • 150
0
votes
0
answers
108
views
0
answers
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 F • 150
0
votes
0
answers
108
views
0
answers
... 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 days ago by
Lina F • 150
0
votes
0
answers
160
views
0
answers
... 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 F • 150
0
votes
0
answers
160
views
0
answers
... 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 F • 150
2
votes
0
answers
160
views
0
answers
... 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 weeks ago by
Lina F • 150
0
votes
0
answers
631
views
0
answers
... 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 F • 150
0
votes
1
answer
302
views
1
answers
... 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 F • 150
0
votes
1
answer
302
views
1
answers
... it's GCA_001007165.2 ...
written 12 months ago by
Lina F • 150
2
votes
1
answer
302
views
1
answer
... 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 12 months ago by
Lina F • 150
• updated
12 months ago by
Pierre Lindenbaum ♦ 121k
Latest awards to Lina F
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For SPAdes is running out of memory
Supporter
8 weeks ago,
voted at least 25 times.
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignment?
Popular Question
10 months ago,
created a question with more than 1,000 views.
For SPAdes is running out of memory
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Extracting more features from EMBL files with Biopython
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Generating consensus sequences
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Calling SNPs with samtools: how to specify how many supporting observations are required?
Popular Question
10 months ago,
created a question with more than 1,000 views.
For How to incorporate metadata in 16S amplicon study and identify confounding variables
Popular Question
12 months ago,
created a question with more than 1,000 views.
For SPAdes is running out of memory
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Is the order of records in the bam file produced by bwa the same as the order in the input fastq file?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For SPAdes is running out of memory
Popular Question
17 months ago,
created a question with more than 1,000 views.
For SPAdes is running out of memory
Popular Question
17 months ago,
created a question with more than 1,000 views.
For bwa mem: which parameters to tune to improve alignment?
Popular Question
17 months ago,
created a question with more than 1,000 views.
For How to demultiplex 16S PE Miseq reads?
Popular Question
17 months ago,
created a question with more than 1,000 views.
For How to assemble complex soil metagenome datasets?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Extracting more features from EMBL files with Biopython
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Is the order of records in the bam file produced by bwa the same as the order in the input fastq file?
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Is the order of records in the bam file produced by bwa the same as the order in the input fastq file?
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Is the order of records in the bam file produced by bwa the same as the order in the input fastq file?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1036 users visited in the last hour