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#1 | ||
Junior Member
Location: Athens, GA Join Date: Feb 2019
Posts: 5
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Good morning, BBMappers!
I have been trying to run BBSplit (on my university's computing cluster) to remove host sequences from metatranscriptome data of a gut community. This is the command I am using: Code:
/home/hd55218/BBSplit/bbmap/bbsplit.sh in=/home/hd55218/BBSplit/QualTrimmed_bran11.fasta ref=/home/hd55218/BBSplit/p.americana_genome.fasta,/home/hd55218/BBSplit/Blattabacterium_genome.fasta basename=out_%.fasta outu=/home/hd55218/BBSplit/cleaned_bran11.fasta Quote:
Quote:
Code:
paste - - - - < Qualtrimmed_bran11.fastq | cut -f 1,2 | sed 's/^@/>/' | tr "\t" "\n" > Qualtrimmed_bran11.fasta |
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#2 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,845
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Do you get an error right away or does the program run for some time?
Are these bbmerged reads? Wonder if you should try to do the binning with original fastq data. Is that a possibility? |
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#3 |
Junior Member
Location: Athens, GA Join Date: Feb 2019
Posts: 5
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From what I can tell, the error shows up right away. I only get an email when my job is finished on the cluster, but the log file shows the error appearing right away (right after the reference files are merged).
Yes, these reads were merged with bbmerge. I was under the impression that bbsplit wanted the reads as FASTA files, but I will try with the FASTQ files! Thank you, and I will let you know how it goes! |
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#4 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,845
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BBSplit will take fastq reads and bin them. Let me know how that works.
You can convert the merged fastq reads afterwards with Code:
reformat.sh in=merged.fq.gz out=merged.fa |
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#5 | |
Junior Member
Location: Athens, GA Join Date: Feb 2019
Posts: 5
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Unfortunately, I get the same assertion error as before when I use my FASTQ file.
The first few sequences of the FASTQ file: Quote:
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#6 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,845
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Can you validate your fastq files to make sure there are no errors in the file?
Use validateFiles from Kent Utilities (UCSC). Linux version linked. After download add execute permissions (chmod a+x validateFiles) before running. validateFiles -type=fastq file1.gz file2.gz etc |
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#7 | ||
Junior Member
Location: Athens, GA Join Date: Feb 2019
Posts: 5
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I used
Code:
validateFiles -type=fastq QualTrimmed_bran11.fastq Quote:
Code:
validateFiles -type=fastq QualTrimmed_bran11.fasta Quote:
(I am using v38.22) Last edited by PinkTips; 02-12-2019 at 11:31 AM. Reason: forgot to add |
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#8 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,845
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I am wondering if the error you are seeing is a red herring. How much memory are you allocating to this job on the cluster (bbsplit can need a lot of memory depending on size of the reference genomes).
You should explicitly add "-Xmx20g" (this is 20 gig, just an example) flag to your bbsplit command. Make sure you match the sample amount of memory on the cluster side. On a side note: Code:
validateFiles -type=fastq QualTrimmed_bran11.fasta Code:
validateFiles -type=fasta QualTrimmed_bran11.fasta |
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#9 |
Junior Member
Location: Athens, GA Join Date: Feb 2019
Posts: 5
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I was only allotting 2GB from the cluster side, likely not enough for BBSplit to do its thing!
I've tried again with "-Xmx200gb" and will let you know how it goes! Thanks - I never would have gotten that from java's error message! |
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Tags |
bbsplit, invalid file format |
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