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Old 03-23-2010, 04:08 AM   #1
Nicolas902
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Location: France

Join Date: Feb 2010
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Default bowtie error "Error reading _offs[] array: "

Dear all,

I am struggling with a bowtie error which occurs in the ebwt.h, here is the code:

Code:
else {
						// Do it all in one read
						MM_READ_RET r = MM_READ(_in2, (void*)this->_offs, offsLen << 2);
						if(r != (MM_READ_RET)(offsLen << 2)) {
							cerr << "Error reading _offs[] array: " << r << ", " << (offsLen << 2) << endl;
							throw 1;
						}
					}
I have built an index using a regular fasta file of hg18 downloaded form ucsc and a splice.fa file generated using ERANGE. bowtie-build is running without any error, as well as "getsplicefa.py" which generates the splice file.

Any idea what this error means?

Thank you.
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Old 05-28-2010, 05:58 AM   #2
anecsulea
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Location: Lausanne

Join Date: Dec 2009
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Hi,

I've been having a similar error. I'm building a bowtie index for a genome sequence, bowtie-build finishes without error, but when trying to align reads with bowtie I get this error:

"Error reading ebwt array: returned 41750080, length was 168445184
Your index files may be corrupt; please try re-building or re-downloading. "

Have you found a solution to the problem ? All suggestions would be appreciated.

Best,

Anamaria
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Old 05-28-2010, 06:29 AM   #3
Nicolas902
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If I remember well, this was a question of directory. I moved the chromosomes sequences I used to the "bowtie" directory.

I hope this was the solution, tell me if it makes it for you.
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Old 05-28-2010, 08:08 AM   #4
anecsulea
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No, this can't be it... For me, this error occurs while running TopHat, and in the TopHat run the fasta file and the bowtie index files are in the same directory.
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Old 08-12-2010, 05:24 AM   #5
Ms@New
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Hi, I get the same error, and I'm using hg18 index from bowtie website.

Did you figure out what was the problem?
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Old 08-27-2010, 09:02 AM   #6
anecsulea
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I don't know what the problem was, but I think I did find a solution: see
http://seqanswers.com/forums/showthread.php?t=5318

Let me know if you need more help on this.

Quote:
Originally Posted by Ms@New View Post
Hi, I get the same error, and I'm using hg18 index from bowtie website.

Did you figure out what was the problem?
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