pslFilter error

[Jasmine Brown]

Hello. I am currently trying to determine the best queries to use from my blat output.psl file.

I used pslFilter and it worked on two of my files however, on the third file it returned this error :

[jbrown@master Blat]$ pslFilter AotusBlat.psl AotusFilter.psl
Filtering AotusBlat.psl to AotusFilter.psl
sizeOne tStarts 4 bs 9
pslFilter: psl.c:77: pslLoad: Assertion `sizeOne == ret->blockCount' failed.

I'm not sure if there is something wrong with my AotusBlat.psl file or what it means by blockCount failed. When I looked at the Aotus.FIlter.psl file it only shows 3 queries so I'm assuming pslFilter did not finish running. Help would be greatly appreciated.

Thanks,

Jasmine N. Brown, MS
PhD Student

Batzer Laboratory of Comparative Genomics
https://biosci-batzerlab.biology.lsu.edu/

Department of Biological Sciences
A653 Life Sciences Building
Louisiana State University
Baton Rouge, LA, 70803

[Luvina Guruvadoo]

Hello Jasmine,

Thank you for your question. For each alignment row in a psl file, there is a blockCount which must match the number of comma-separated values in blockSizes, qStarts, and tStarts. In this particular error, it says that the blockCount is 9, but there are only 4 comma-separated values in the tStarts column. We could take a closer look if you would like to send us your psl file.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Jasmine Brown]

Hello. Thank you for your response. I have attached my .psl file that was giving me the following error.

[jbrown@master Blat]$ pslFilter AotusBlat.psl AotusFilter.psl
Filtering AotusBlat.psl to AotusFilter.psl
sizeOne tStarts 4 bs 9
pslFilter: psl.c:77: pslLoad: Assertion `sizeOne == ret->blockCount' failed.

Jasmine N. Brown, MS
PhD Student

Batzer Laboratory of Comparative Genomics
https://biosci-batzerlab.biology.lsu.edu/

Department of Biological Sciences
A653 Life Sciences Building
Louisiana State University
Baton Rouge, LA, 70803

[Steve Heitner]

Hello, Jasmine.

My colleague Luvina pointed out previously that there was an entry in your file that specified a blockCount of 9, but only had four comma-separated values in the tStarts column.  This is the case with the very last entry in the file.  I added some dummy data to the end of the file so the tStarts column had 9 comma-separated values and pslFilter ran without error.

The problematic entry does not have a trailing comma, nor is there a newline at the end of the file which suggests that your file was somehow truncated.  You will probably want to re-run whatever process you used to create the file to generate a complete file.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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