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Old 05-13-2013, 09:27 PM   #1
PBM
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Location: india

Join Date: May 2013
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Default TopHat2 run error

Hi All,

Whenever I run tophat2 it fails in the following section:

[2013-05-14 10:25:41] Mapping left_kept_reads to genome chr2.fa with Bowtie2
[FAILED]
Error running bowtie:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc


I have tophat 2.0.8b,bowtie 2.1.0.0, samtools 0.1.19.0 versions of the tools

It would be great if some one can guide me for the same.

Thanks
PB
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Old 05-14-2013, 01:31 AM   #2
ron128
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Can you check the diskspace where the files are running? TOphat requires a lot of temporary space when its running and may give errors if the diskspace is full. Alternatively, have you tried running the older version of bowtie and troubleshooting this issue? I have never come accross such an issue in my runs.

The std:bad alloc error is generally thrown up when there are memory allocation issues. Are you sure there is enough memory available on your system to carry out these computations?
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Old 05-14-2013, 07:07 PM   #3
PBM
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Quote:
Originally Posted by ron128 View Post
Can you check the diskspace where the files are running? TOphat requires a lot of temporary space when its running and may give errors if the diskspace is full. Alternatively, have you tried running the older version of bowtie and troubleshooting this issue? I have never come accross such an issue in my runs.

The std:bad alloc error is generally thrown up when there are memory allocation issues. Are you sure there is enough memory available on your system to carry out these computations?
The system has 1 TB RAM and 2TB diskspace available.
Memory usage during Tophat run didnot exceed 27GB.

Is their any particular combination of Tophat and Bowtie version that needs to be installed?
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Old 05-20-2013, 10:31 PM   #4
ron128
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Quote:
Originally Posted by PBM View Post
The system has 1 TB RAM and 2TB diskspace available.
Memory usage during Tophat run didnot exceed 27GB.

Is their any particular combination of Tophat and Bowtie version that needs to be installed?
Is the 2 Tb of diskspace uniformly allocated? If there is lesser space on your home folder, this may affect the writing of files in tmp directory. At least the memory is not a constraint in this case. My pipeline makes use of Tophat 2.0 and Bowtie 1.0 I have used TOphat 2.0 along with Bowtie 2.0 but have not faced this issue time. can you share your command line arguments here for ppl to troubleshoot.
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