Assertion failed error in BFAST localalign

seeker · 09-02-2011, 06:31 AM

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 · 09-02-2011, 08:02 AM

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 · 09-02-2011, 11:02 AM

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 · 09-02-2011, 05:17 PM

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

nilshomer · 09-02-2011, 07:25 PM

Where are you getting your FASTQ from?

seeker · 09-02-2011, 08:05 PM

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 · 09-02-2011, 08:07 PM

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

seeker · 09-02-2011, 10:33 PM

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?

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09-02-2011, 06:31 AM	#1
seeker Member Location: Zurich Join Date: Jan 2011 Posts: 26	Assertion failed error in BFAST localalign 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

09-02-2011, 08:02 AM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	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.

09-02-2011, 11:02 AM	#3
seeker Member Location: Zurich Join Date: Jan 2011 Posts: 26	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?

09-02-2011, 05:17 PM	#4
seeker Member Location: Zurich Join Date: Jan 2011 Posts: 26	Changed the name and still the same error. How could I ensure that all the names are in the same order?

09-02-2011, 07:25 PM	#5
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Where are you getting your FASTQ from?

09-02-2011, 08:05 PM	#6
seeker Member Location: Zurich Join Date: Jan 2011 Posts: 26	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.

09-02-2011, 08:07 PM	#7
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Ah, you have to make them together. You cannot convert them unpaired then input them as paired.

09-02-2011, 10:33 PM	#8
seeker Member Location: Zurich Join Date: Jan 2011 Posts: 26	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?