BAM file cannot be parsed

Martin Abba

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Apr 28, 2013, 6:38:10 PM4/28/13

to asammate

Hi,

I am SAMMAte's user. I am trying to run sammate 2.7.4 using linux from
the command line but with unsuccessful results. I get the following
message error in the terminal (see below).

Do you have some suggestion about it?

Best regards from Buenos Aires - Argentina

Martin

mcabba@s855:~/Desktop/RNAseqlibraries$ sh SAMMate.sh -m RAEM -a
Homo_sapiens.gtf -i 93VU.bam,BHY.bam,BICR22.bam,Cal27.bam,Cal33.bam -o
test
/home/mcabba/Desktop/RNAseqlibraries/
18:14:40 <INFO> Start parsing annotation file Homo_sapiens.gtf in
GTF format...
18:14:50 <INFO> Parsing annotation file is complete.
18:14:50 <INFO> Start parsing alignment results of 93VU.bam in BAM
format...
18:29:26 <ERROR> The BAM file cannot be parsed due to invalid
format, the following row cannot be parsed:
18:29:26 <ERROR> C0AUEACXX:5:1101:02628:127637
18:29:26 <ERROR> The BAM file cannot be parsed due to invalid
format.
java.lang.NullPointerException
at
Wayne.CS.CBDM.alignment.BAMJunctionParser.updateGenes(BAMJunctionParser.java:
222)
at
Wayne.CS.CBDM.alignment.BAMJunctionParser.parseFile(BAMJunctionParser.java:
140)
at Wayne.CS.CBDM.calculator.TaskExecutor.parseFile(TaskExecutor.java:
314)
at Wayne.CS.CBDM.calculator.TaskExecutor.run(TaskExecutor.java:181)
at
Wayne.CS.CBDM.calculator.TaskExecutor.executeTasks(TaskExecutor.java:
149)
at Wayne.CS.CBDM.ui.Startup.executeTasks(Startup.java:102)
at Wayne.CS.CBDM.ui.Startup.main(Startup.java:62)
18:29:26 <INFO> The total count of short reads mapped on exon-exon
juntions is : 0
18:29:26 <INFO> The total count of short reads mapped on exons is :
49352963
18:29:26 <INFO> The total count of reads is : 49352963
18:29:26 <INFO> Parsing BAM file is complete.
18:29:26 <INFO> Start estimating transcript expression abundance
using RAEM procedure.
18:29:26 <ERROR> Function EMEstimator.calculate:
java.lang.NullPointerException

Tin Nguyen Chi

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Apr 28, 2013, 8:05:02 PM4/28/13

to asam...@googlegroups.com

Hi,

From the log, I don't know the reason. May you please try on the windows/MAC version and see what happens? Another solution is to give the test file so I can try to debug it

Thanks

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Dongxiao Zhu

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Apr 28, 2013, 8:09:31 PM4/28/13

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Thanks, Tin. I gave the metagenomics talk and it was great.

Please keep working on the BCB paper, and send me the most recent version.

Dongxiao

From: "Tin Nguyen Chi" <tin.ng...@gmail.com>
To: asam...@googlegroups.com
Sent: Sunday, April 28, 2013 8:05:02 PM
Subject: Re: BAM file cannot be parsed

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