Hi all,
I was aligning paired end reads in two fastq files: read_1.fq and read_2.fq generated from the grinder simulation program and kept the alignments in read_1.sai and read_2.sai files. Then I tried to combine them into one bam file by:
bwa sampe ../../CP000948.fna read_1.sai read_2.sai read_1.fq read_2.fq >read_12.sam
It will be a success when read_1.fq and read_2.fq are all properly paired (every read in 1 has a mate in 2) but it will report following error when I artificially remove one read from 1 (making one pair missing an end):
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[fread] Unexpected end of file
My purpose of doing this is the fq files generated from grinder behave this way. Although their paper don't touch on this, I guess its one of the possible error mechansims they try to simulate. But this is causing trouble in the downstream bwa pipeline. Just wonder if this is a normal bwa sampe behavior and is there any mature tools out there for taking care of this. It is probably better than I manually write a more error-prone script to fix it myself.
Thanks a lot!
I was aligning paired end reads in two fastq files: read_1.fq and read_2.fq generated from the grinder simulation program and kept the alignments in read_1.sai and read_2.sai files. Then I tried to combine them into one bam file by:
bwa sampe ../../CP000948.fna read_1.sai read_2.sai read_1.fq read_2.fq >read_12.sam
It will be a success when read_1.fq and read_2.fq are all properly paired (every read in 1 has a mate in 2) but it will report following error when I artificially remove one read from 1 (making one pair missing an end):
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[fread] Unexpected end of file
My purpose of doing this is the fq files generated from grinder behave this way. Although their paper don't touch on this, I guess its one of the possible error mechansims they try to simulate. But this is causing trouble in the downstream bwa pipeline. Just wonder if this is a normal bwa sampe behavior and is there any mature tools out there for taking care of this. It is probably better than I manually write a more error-prone script to fix it myself.
Thanks a lot!
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