Entering edit mode
3.3 years ago
samantharenee98
•
0
I am trying to align SRA to a mitochondrial reference genome that has been pulled in fasta form from NCBI. The output I keep getting is not normal, its going through it in 0.023 seconds.
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.5a-r405
[main] CMD: bwa index -a is ref_genome/sequence.fasta
[main] Real time: 0.009 sec; CPU: 0.023 sec
then nothing else works beyond this. I will get an error about not being able to retrieve the indexed file..
I dont know if this is a good enough explanation and I am definitely new to this, so thank you for your patience.
I can follow up with any other info if necessary.
Hello, please show the code you run, without that and the error message this is not reproducible.
So sorry.
bwa index ref_genome/sequence.fasta
andbwa index sequence.fasta
and ive also done
Output:
and
Output:
I see no error here.
what is the output of
Yes, that is the normal indexing output, but you say:
so there must be more code that you run, so the actual alignment?
This is what ive done after that indexing.
No output
Output:
Also just want to thank you all for you fast responses!
First things I'd check are that the formats of your fastqs and fastqs are okay.
Odd, what is the output of
head data/fundhe.fastq
andwc -l data/fundhe.fastq
? Looks like either the files are empty or corrupted because the first line of flagstat would also show unmapped reads and I guess if the index was corrupted bwa would complain as well, so it is probably the fastq being off as @swbarnes2 says.