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40 threads, 800G memory.
40 threads, 800G memory.
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I have a feeling the job is hung. Is this under a job scheduler? In my experience, bbduk starts writing output even when running under a scheduler right away.Comment
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It was submitted to a server with a scheduler, yes.
It's just odd that it's the exact same code and dataset, but the only difference is hdist=1...same set up with hdist=0 runs fine.Comment
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Are you able to ssh to the node this is job is on and see if the bbduk is running (something like top -H)?Comment
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The java process (should correspond to bbduk) appears to be sleeping (at least in this screenshot). Does it change back to R periodically or is it staying in S?
@Brian had talked about memory requirements with hdist=1 before. It may not be applicable in your case.Comment
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Based on a minute of observation, it appears to be sleeping, however the %CPU and %MEM change as I re-issue 'top'.Comment
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Based on Brian's comments, I bet I have run out of memory. My reference is very large, and a 3*K increase in memory would put me over my server capacity. I will try to re-run with a smaller reference.Comment
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Unless your scheduler is buffering the entire output in some temp location you should have seen trimmed files right away (have you ever looked before if a job does that)? Did you try top -H to see all ~40 java threads?
Based on your last comment that must be the case.Comment
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reads mapped per gene
Hi,
can you suggest how to get raw reads mapped per gene from bbmap?
Thanks,
S.Comment
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Based on your other posts you appear to have discovered htseq-count and featureCounts. BBMap suite does not have a read counting program (though @Brian has one on the wishlist of things to add to BBMap).Originally posted by susanklein View PostComment
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hi! is there a way to extract specific sequences from fasta file, regarding their positions in the file using BBMap tools? I know the numbers of their name lines and want to extract whole sequences to a file.Comment
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It is not clear if you know their identifiers (or just their positions). If you have the identifiers then you can do the followingOriginally posted by JeanLove View Post
Even though this example is for fastq files I am reasonsably certain that it would work for fasta. Make sure your file names end in .fa to facilitate that.By default, "filterbyname" discards reads with names in your name list, and keeps the rest. To include them and discard the others, do this:
Code:$ filterbyname.sh in=003.fastq out=filter003.fq names=names003.txt include=t
In case BBMap does not work you can try faSomeRecords utility from Jim Kent @UCSC which is described here: http://seqanswers.com/forums/showthread.php?t=64004Comment
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If you know the sequence numbers, you can use getreads.sh:
Usage: getreads.sh in=<file> id=<number,number,number...> out=<file>
The first read (or pair) has ID 0, the second read (or pair) has ID 1, etc.
Parameters:
in=<file> Specify the input file, or stdin.
out=<file> Specify the output file, or stdout.
id= Comma delimited list of numbers or ranges, in any order.
For example: id=5,93,17-31,8,0,12-13Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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