Question: Tophat Slow : Searching For Junctions Via Segment Mapping
0
gravatar for Nicolas Rosewick
7.2 years ago by
Belgium, Brussels
Nicolas Rosewick7.9k wrote:

Hi,

Is it normal that my tophat jobs are running the step "Searching for junctions via segment mapping" since 4 days ? I'm running tophat2 with 76 bp paired-end reads with -p 4 and 15Gb of memory. here's my log file :

[2012-05-03 11:19:56] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-03 11:19:56] Checking for Bowtie
          Bowtie version:     2.0.0.5
[2012-05-03 11:19:56] Checking for Samtools
        Samtools version:     0.1.18.0
[2012-05-03 11:19:56] Checking for Bowtie index files
[2012-05-03 11:19:56] Checking for reference FASTA file
[2012-05-03 11:19:56] Generating SAM header for DB
    format:         fastq
    quality scale:     phred33 (default)
[2012-05-03 11:20:00] Preparing reads
     left reads: min. length=76, count=14027314
    right reads: min. length=76, count=14048352
[2012-05-03 11:34:13] Mapping left_kept_reads against DB with Bowtie2 
[2012-05-03 13:07:51] Mapping left_kept_reads_seg1 against DB with Bowtie2 (1/3)
[2012-05-03 13:59:08] Mapping left_kept_reads_seg2 against DB with Bowtie2 (2/3)
[2012-05-03 14:58:46] Mapping left_kept_reads_seg3 against DB with Bowtie2 (3/3)
[2012-05-03 16:02:58] Mapping right_kept_reads against DB with Bowtie2 
[2012-05-03 17:37:00] Mapping right_kept_reads_seg1 against DB with Bowtie2 (1/3)
[2012-05-03 18:24:02] Mapping right_kept_reads_seg2 against DB with Bowtie2 (2/3)
[2012-05-03 19:16:00] Mapping right_kept_reads_seg3 against DB with Bowtie2 (3/3)
[2012-05-03 20:25:54] Searching for junctions via segment mapping

Anyone has the same problem ?

Thanks

tophat • 3.3k views
ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Nicolas Rosewick7.9k
1

Does the output of "top" show that the process is actually using compute resources? What is the memory usage showing?

ADD REPLYlink written 7.2 years ago by Sean Davis25k

here's when I do a qstat on my sge job : cpu=17:10:27:53, mem=2525712.89942 GBs, io=544.86174, vmem=2.282G, maxvmem=4.171G. I don't know how to know the memory usage in real time (like in Top) on a sge grid

ADD REPLYlink modified 7.2 years ago • written 7.2 years ago by Nicolas Rosewick7.9k
1

I should have been less specific. The question is whether your job is swapping. You may need to ask a system administrator for help in answering this question.

ADD REPLYlink written 7.2 years ago by Sean Davis25k
0
gravatar for Nicolas Rosewick
7.2 years ago by
Belgium, Brussels
Nicolas Rosewick7.9k wrote:

I think I found the problem. On of my job successfully ended this morning. But when I check the sge log file, I observed that the job used : Max vmem = 20.210G but I only allowed 15Go for the job. So I think it will use a lot of swap in/ swap out time to finish the process. I will try with much more memory .

ADD COMMENTlink written 7.2 years ago by Nicolas Rosewick7.9k
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