bfast localalign issues

[yy01]

Hi, anyone has an idea what causes this error?
Please, help!

Thanks in advance.


bfast localalign -f mature_converted.fa -m bfast.matches.s_1_1_sequence_clean.bmf > bfast.aligned.s_1_1_sequence_clean.baf
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName mature_converted.fa.
Validating matchFileNamebfast.matches.s_1_1_sequence_clean.bmf.
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: mature_converted.fa
matchFileName: bfast.matches.s_1_1_sequence_clean.bmf
matchFileNameOne: [Not Using]
matchFileNameTwo: [Not Using]
scoringMatrixFileName: [Not Using]
ungapped: [Not Using]
unconstrained: [Not Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
offsetLength: 20
maxNumMatches: 384
avgMismatchQuality: 10
numThreads: 1
queueLength: 10000
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from mature_converted.fa.nt.brg.
In total read 17341 contigs for a total of 377003 bases
************************************************************
************************************************************
Reading match file from bfast.matches.s_1_1_sequence_clean.bmf.
************************************************************
Performing alignment...
Reads processed: 0bfast: RGMatches.c:91: RGMatchesRead: Assertion `m->readNameLength < 4028' failed.
Aborted

[nilshomer]

Looks like you may have some file corruption as the read name check should have been caught at the match step if it was real. Re-run the match process, and if that does not work, post to bfast-help@lists.sourceforge.net

[yy01]

Thanks, Nils!
Matches were re-run, and everything went through smoothly for running localalign.

-Yanming

[xinwu]

Originally Posted by nilshomer

Looks like you may have some file corruption as the read name check should have been caught at the match step if it was real. Re-run the match process, and if that does not work, post to bfast-help@lists.sourceforge.net

I met the same issue. After rerun it, It still threw this exception. I tested the data with Bowtie, it worked. So, what is the read name check? and why it failed in this step? Thanks.

[nilshomer]

Originally Posted by xinwu

I met the same issue. After rerun it, It still threw this exception. I tested the data with Bowtie, it worked. So, what is the read name check? and why it failed in this step? Thanks.

The read name cannot be longer than 4028 characters.

[xinwu]

Originally Posted by nilshomer

The read name cannot be longer than 4028 characters.

Thanks for the quick reply, Nils. But I am sure the name should not exceed
4028 which is really a large number for a name. There must be something wrong somewhere.

[nilshomer]

There definitely is. Could you try aligning subsets of your reads until you can identify the problem read? That is how I would begin to debug this problem.

[xinwu]

Originally Posted by nilshomer

There definitely is. Could you try aligning subsets of your reads until you can identify the problem read? That is how I would begin to debug this problem.

I've checked all read names, the max length of them is 37. I've tried a small set with 1000 reads, it worked fine. The original reads file is about 7G with ~130M reads (100bp). Does its size matter?

[nilshomer]

Originally Posted by xinwu

I've checked all read names, the max length of them is 37. I've tried a small set with 1000 reads, it worked fine. The original reads file is about 7G with ~130M reads (100bp). Does its size matter?

It shouldn't matter no. Try breaking it up into chunks of 1M reads, then processing them separately.