Assertion failed error in BFAST localalign

[seeker]

Hi all, I'm getting the following error when trying to combine bfast and bwa mapped reads. Any suggestions would be appreciated.

command:
bfast localalign -f rna.fasta -1 p1.f3.reads.bmf -2 p1.f5.reads.bfm -A 1 -t -U -n 4 > p1.reads.baf

error:
Assertion failed: (0 == strcmp(m->readName, r2_name)), function RGMatchesRead_2bmf, file RGMatches.c, line 51.
Abort trap
Assertion failed: (0 == strcmp(m->readName, r2_name)), function RGMatchesRead_2bmf, file RGMatches

[nilshomer]

Looks like your reads are not in the same order within the two files (also p1.f5.reads.bfm should be p1.f5.read.bmf). Take a look at your input FASTQ files to make sure the read names are in the same order.

[seeker]

The first and last 100 lines of reads are in the same order. I've renamed the f5 files to bmf (which was a typo when making the files). Could that be responsible?

[seeker]

Changed the name and still the same error. How could I ensure that all the names are in the same order?

[nilshomer]

Where are you getting your FASTQ from?

[seeker]

From the solid2fastq script that came with bfast+bwa. I made a seperate fastq for each of the F3 and F5 reads rather than paired.

[nilshomer]

Ah, you have to make them together. You cannot convert them unpaired then input them as paired.

[seeker]

Oh, I was following the flow from here: http://seqanswers.com/forums/showthr...ight=bfast+bwa

So, you make the fastq paired, then map using the same fastq file for the f3 and f5 seperately?