Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences

Similar Threads
Thread Thread Starter Forum Replies Last Post
Systemic problem with PacBio data and chimeric contigs k-gun12 Pacific Biosciences 8 05-03-2017 08:18 AM
pacbio reads alignment Rui Guo Pacific Biosciences 1 05-19-2016 08:21 AM
PacBio data - problem with SRA toolkit Retro Pacific Biosciences 7 12-04-2015 05:56 AM
samstat versus tophat overall alignment rate % alyamahmoud RNA Sequencing 1 12-26-2013 07:11 AM
Samstat error message pmgr RNA Sequencing 0 06-12-2013 01:21 AM

Thread Tools
Old 08-01-2017, 10:24 AM   #1
Junior Member
Location: USA

Join Date: Jun 2017
Posts: 2
Default problem with samstat on PacBio alignment

Dear all,
I ran an alignment of Sequel data using blasr. Now I want to get some metrics about the sam file using samstat 1.5.1 (running on Ubuntu 16.04 LTS; 16 Gb of RAM).
I get a message that reads:

[2017-08-01 13:26:25] SAMstat 1.5.1, Copyright (C) 2014 Timo Lassmann <[email protected]>
[2017-08-01 13:26:25] cmd: samstat Ecoli_2K.sam
[2017-08-01 13:26:25] Ecoli_2K.sam
[2017-08-01 13:26:25] Starting to collect data.
[2017-08-01 13:26:25] Training a HMM on mapq > 20 reads.
Segmentation fault (core dumped)

I suspect the problem is the file size (>150,000 reads, file size: 13.5 Gb), so I trimmed the sam file using "head -n". I am only successful at getting a report when I have 20 reads...

{I have no problem getting a report when I work with Illumina-based alignments}

Is this a PacBio-specific problem?
Is the problem the memory? is there a way to increase the RAM usage of samstat (similar to a -vm function in some Java applications)?
is there another solution? Are there other programs out there that can do the same as samstat 1.5 (the reports are very cool!)?



PS: there is the same kind of problem if the alignment is done with BWA MEM...
drkijak is offline   Reply With Quote
Old 08-01-2017, 11:49 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,660

What kind of statistics are you looking for? Perhaps Qualimap may work instead.
GenoMax is offline   Reply With Quote
Old 08-02-2017, 12:20 PM   #3
Junior Member
Location: USA

Join Date: Jun 2017
Posts: 2

Thanks GenoMax! I wanted to get some qmap summary (the piechart at the top of the samstat report). I may need to script it with Rsamtools...

I think that samstat and qualimap complement each other.
drkijak is offline   Reply With Quote

blasr, pacbio, samstat, sequel

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:23 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO