Maybe someone can see what I'm doing wrong here. I'm using BWA to align a dataset and get a SAM file that I can use for variant calling. I've indexed the reference fasta file with 'bwa index' and run 'bwa aln' to generate my .sai files. These steps seem to have worked, but when I try to use 'bwa sampe' to produce a .sam file, the process aborts and I get the following error message:
'[bns_restore_core] fail to open file 'human_g1k_v37.fasta.ann'. Abort!'
The command I'm using is:
'bwa sampe -a 500 -o 100000 -n 3 -N 10 -P human_g1k_v37.fasta ERR035484_1.sai ERR035484_2.sai ERR035484_1.fastq ERR035484_2.fastq > PEA1.sam'
I have a .ann file ('human_g1k_v37.ann') from the indexing step, and I thought it might be a filename problem, i.e. the program trying to open a .fasta.ann file instead of just .ann, but omitting the .fasta in the command still gave a similar error message.
The first few lines of my .ann file look like this:
3101804739 84 11
0 1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
0 249250621 39
0 2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
249250621 243199373 24
0 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
492449994 198022430 9
0 4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
690472424 191154276 12
0 5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
I've searched the forum but not found a solution to this that works for me. Can anyone help me out?
'[bns_restore_core] fail to open file 'human_g1k_v37.fasta.ann'. Abort!'
The command I'm using is:
'bwa sampe -a 500 -o 100000 -n 3 -N 10 -P human_g1k_v37.fasta ERR035484_1.sai ERR035484_2.sai ERR035484_1.fastq ERR035484_2.fastq > PEA1.sam'
I have a .ann file ('human_g1k_v37.ann') from the indexing step, and I thought it might be a filename problem, i.e. the program trying to open a .fasta.ann file instead of just .ann, but omitting the .fasta in the command still gave a similar error message.
The first few lines of my .ann file look like this:
3101804739 84 11
0 1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
0 249250621 39
0 2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
249250621 243199373 24
0 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
492449994 198022430 9
0 4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
690472424 191154276 12
0 5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
I've searched the forum but not found a solution to this that works for me. Can anyone help me out?
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