problem with samstat on PacBio alignment

drkijak · 08-01-2017, 11:24 AM

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 <timolassmann@gmail.com>
[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!)?

Thanks,

Gustavo

PS: there is the same kind of problem if the alignment is done with BWA MEM...

GenoMax · 08-01-2017, 12:49 PM

What kind of statistics are you looking for? Perhaps Qualimap may work instead.

drkijak · 08-02-2017, 01:20 PM

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.

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08-01-2017, 11:24 AM	#1
drkijak Junior Member Location: USA Join Date: Jun 2017 Posts: 2	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 <timolassmann@gmail.com> [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!)? Thanks, Gustavo PS: there is the same kind of problem if the alignment is done with BWA MEM...

08-01-2017, 12:49 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	What kind of statistics are you looking for? Perhaps Qualimap may work instead.

08-02-2017, 01:20 PM	#3
drkijak 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.