Problem of Paired-end data processing

GoogleCodeExporter commented 8 years ago

My data is paired-end reads,but when i use the -a -b options,the program said 
as follows 
===========================================================
Start at:  Thu Nov 18 23:10:33 2010

Load in 5 db seqs, total size 119146348 bp. 4 secs passed
total_kmers: 59049
Create seed table. 13 secs passed
Pair-end alignment:
Query: ../../ara2010bsseq/SRR042638_1.fastq  
/home/bioinformatics/xie/methy_seq/ara2010bsseq/SRR042638_2.fq  Reference: 
/home/bioinformatics/data/arbidopsis/genome.fa  Output: bsmap_ara_pe
failed to open file:

===============================================================
And when I use only -a option,it works well.I don't understand why!
Could somebody give me some suggestions?
My email address:327696170@qq.com

Original issue reported on code.google.com by xieshaoj...@gmail.com on 18 Nov 2010 at 8:13

GoogleCodeExporter commented 8 years ago

I'm seeing the same issue with my paired end data.

Original comment by cwhe...@gmail.com on 31 Jan 2011 at 7:14

GoogleCodeExporter commented 8 years ago

I poked around in the code a little and found that you can get past this error 
by making sure that you specify an output file for unpaired reads using the -2 
option.

Unfortunately I now get a segmentation fault, but at least I got past that 
point.

Original comment by cwhe...@gmail.com on 1 Feb 2011 at 7:07

GoogleCodeExporter commented 8 years ago

My data is paired-end reads,but when I used "-b", the program said "unknown 
option: –b".Could somebody give me some suggestions?

Original comment by wangyiha...@gmail.com on 16 Jul 2015 at 2:54

popucui / bsmap

Problem of Paired-end data processing #6