Hi,
I gave this simple command
bowtie2 -x /path/to/my/index -1 fastq1 -2 fastq2 -S output.sam
resultant:
Error: Encountered Internal Bowtiw 2 exception (#1)
Command: bowtie2 -x /path/to/my/index -1 fastq1 -2 fastq2 -S output.sam
(ERR): bowtie2-align exited with value 1
I have tried bowtie2-align as well with -l and -s switches. My index files are properly created with all 6 .bt2 files
Kindly help me sort this out.
Regards, Qurat
You probably are but just to check: Are you using the correct
basename
for the index files?I'd given the basename while indexing as "xyz_index". It created following files:
xyz_index.1.bt2 xyz_index.2.bt2 xyz_index.3.bt2 xyz_index.4.bt2 xyz_index.rev.1.bt2 xyz_index.rev.2.bt2
What version of bowtie2 are you using? If it is not the latest then the first thing to try would be to upgrade. Has this index been successfully used before for other alignments?
Its bowtie2-align-s version 2.2.6
I have been using the said version before. Its just that i completed the indexing a few hours back and tried the alignment but it wont let me move ahead.
i did try bowtie2-align, where it would give the error about the -l or -s switch usage.
Using either one of them gives the error pertaining the warning that, "Bowtie 2-align was un directly. it is recommended that you run the wrapper script bowtie 1 instead"
but then using bowtie2 alone, still gives the error but in the above given manner.
Please use
ADD COMMENT/ADD REPLY
when responding to existing posts to keep threads logically organized.Try just one of the fastq files, perhaps one of them has an error.