Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #91
    There is no output yet...

    40 threads, 800G memory.

    Comment


    • #92
      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


      • #93
        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


        • #94
          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


          • #95

            Comment


            • #96
              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


              • #97
                Based on a minute of observation, it appears to be sleeping, however the %CPU and %MEM change as I re-issue 'top'.

                Comment


                • #98
                  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


                  • #99
                    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


                    • reads mapped per gene

                      Hi,

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

                      Thanks,

                      S.

                      Comment


                      • Originally posted by susanklein View Post
                        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).

                        Comment


                        • 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


                          • Originally posted by JeanLove View Post
                            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:

                            Code:
                            $ 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

                            Comment


                            • Originally posted by GenoMax View Post
                              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..


                              Originally posted by GenoMax View Post
                              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!

                              Comment


                              • 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

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Choosing Between NGS and qPCR
                                  by seqadmin



                                  Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
                                  10-18-2024, 07:11 AM
                                • seqadmin
                                  Non-Coding RNA Research and Technologies
                                  by seqadmin




                                  Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

                                  Nobel Prize for MicroRNA Discovery
                                  This week,...
                                  10-07-2024, 08:07 AM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, Yesterday, 05:31 AM
                                0 responses
                                10 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 10-24-2024, 06:58 AM
                                0 responses
                                20 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 10-23-2024, 08:43 AM
                                0 responses
                                48 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 10-17-2024, 07:29 AM
                                0 responses
                                58 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X