[jazz710]

There is no output yet...

40 threads, 800G memory.

[GenoMax]

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.

[jazz710]

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.

[GenoMax]

Are you able to ssh to the node this is job is on and see if the bbduk is running (something like top -H)?

[jazz710]

[GenoMax]

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.

[jazz710]

Based on a minute of observation, it appears to be sleeping, however the %CPU and %MEM change as I re-issue 'top'.

[jazz710]

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.

[GenoMax]

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.

[susanklein]

reads mapped per gene

Hi,

can you suggest how to get raw reads mapped per gene from bbmap?

Thanks,

S.

[GenoMax]

Hi,

can you suggest how to get raw reads mapped per gene from bbmap?

Thanks,

S.

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).

[JeanLove]

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.

[GenoMax]

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.

It is not clear if you know their identifiers (or just their positions). If you have the identifiers then you can do the following

By default, "filterbyname" discards reads with names in your name list, and keeps the rest. To include them and discard the others, do this:

$ filterbyname.sh in=003.fastq out=filter003.fq names=names003.txt include=t

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.

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=64004

[JeanLove]

It is not clear if you know their identifiers (or just their positions). If you have the identifiers then you can do the following[/url]

I do not know identifiers..

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=64004

thanks for your help, i'll look faSomeRecords utility up!

[Brian Bushnell]

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=5,93,17-31,8,0,12-13