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Old 02-09-2010, 10:54 AM   #1
javijevi
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Default BFAST error in FindMatchesInIndexSet function

Hi all,

I successfully went along the first steps of BFAST pipeline, including the indexes creation, but got the below copied error when running 'bfast match' step with the following command for a fastq test file with 9 reads:

bfast match -f reference_genome.fa -A 1 -r test.fastq -i 1 -I 2-10 1> matches.bmf 2> match.log &

Contents of match.log:
(...)
Searching index file 1/1 (index #1, bin #1) complete...
Found 4 matches.
Found matches for 4 reads.
Copying unmatched reads for secondary index search.
Splitting unmatched reads into temp files.
bfast: RunMatch.c:718: FindMatchesInIndexSet: Assertion `numReads == numWritten' failed.
Splitting unmatched reads into temp files.
bfast: RunMatch.c:718: FindMatchesInIndexSet: Assertion `numReads == numWritten' failed.

Any idea?

Thanks in advance.
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Old 02-09-2010, 10:57 AM   #2
javijevi
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Quote:
Originally Posted by javijevi View Post
Splitting unmatched reads into temp files.
bfast: RunMatch.c:718: FindMatchesInIndexSet: Assertion `numReads == numWritten' failed.
Splitting unmatched reads into temp files.
bfast: RunMatch.c:718: FindMatchesInIndexSet: Assertion `numReads == numWritten' failed.
Just to tell that I made a mistake in copying twice the last two lines of the output.
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Old 02-09-2010, 11:57 AM   #3
nilshomer
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Quote:
Originally Posted by javijevi View Post
Hi all,

I successfully went along the first steps of BFAST pipeline, including the indexes creation, but got the below copied error when running 'bfast match' step with the following command for a fastq test file with 9 reads:

bfast match -f reference_genome.fa -A 1 -r test.fastq -i 1 -I 2-10 1> matches.bmf 2> match.log &

Contents of match.log:
(...)
Searching index file 1/1 (index #1, bin #1) complete...
Found 4 matches.
Found matches for 4 reads.
Copying unmatched reads for secondary index search.
Splitting unmatched reads into temp files.
bfast: RunMatch.c:718: FindMatchesInIndexSet: Assertion `numReads == numWritten' failed.
Splitting unmatched reads into temp files.
bfast: RunMatch.c:718: FindMatchesInIndexSet: Assertion `numReads == numWritten' failed.

Any idea?

Thanks in advance.
Any reason why you want to use secondary indexes? I would recommend using all the indexes in the primary search (no secondary indexes).

This may be a bug (with the secondary search). Please submit your report to bfast-help@lists.sourceforge.net so we can resolve the issue quickly.
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Old 02-09-2010, 12:54 PM   #4
nilshomer
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Quote:
Originally Posted by nilshomer View Post
Any reason why you want to use secondary indexes? I would recommend using all the indexes in the primary search (no secondary indexes).

This may be a bug (with the secondary search). Please submit your report to bfast-help@lists.sourceforge.net so we can resolve the issue quickly.
I have found the bug and fixed the latest source code available via GIT. Let me know if you have any problems: )
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Old 02-09-2010, 02:43 PM   #5
javijevi
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Originally Posted by nilshomer View Post
Any reason why you want to use secondary indexes? I would recommend using all the indexes in the primary search (no secondary indexes).
In BFAST book, you can find the following: 'If you wish to have a secondary set of indexes, which are used if no matches are found in the main set of indexes, use the -I option'. So, I thought that it was more efficient to not use a mismatch-allowing index, e.g., 1110111110011111, for reads which were already mapped by using an all-matchs index, that is, 11111111111111.

Obviously, I missed something important in this issue because of the complexity of the index-based search algorithm for a biologist, and I therefore will blindly follow your recommendation about not using secondary indexes.
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Old 02-09-2010, 03:57 PM   #6
nilshomer
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Quote:
Originally Posted by javijevi View Post
In BFAST book, you can find the following: 'If you wish to have a secondary set of indexes, which are used if no matches are found in the main set of indexes, use the -I option'. So, I thought that it was more efficient to not use a mismatch-allowing index, e.g., 1110111110011111, for reads which were already mapped by using an all-matchs index, that is, 11111111111111.

Obviously, I missed something important in this issue because of the complexity of the index-based search algorithm for a biologist, and I therefore will blindly follow your recommendation about not using secondary indexes.
I have spent a lot of time thinking about the indexing strategy and I would follow the strategy found in section 7.1 where we use 10 "main" indexes and no secondary indexes.

I apologize for the confusion but I tried to keep options for flexibility.
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