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Old 08-01-2017, 11:24 AM   #1
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Location: USA

Join Date: Jun 2017
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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 <>
[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, 12:49 PM   #2
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What kind of statistics are you looking for? Perhaps Qualimap may work instead.
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Old 08-02-2017, 01:20 PM   #3
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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

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