Hello, I´m new using Galaxy and would really appreciate some help. I´m trying to run BWA in my local Galaxy and as a result, it's producing an empty file. I get this error:
[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: 0.7.12-r1039
[main] CMD: bwa index localref.fa
[main] Real time: 0.491 sec; CPU: 0.008 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.05 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 10000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln -t 1 localref.fa /etc/galaxy/galaxy/database/files/000/dataset_43.dat
[main] Real time: 0.120 sec; CPU: 0.060 sec
[bwa_aln_core] convert to sequence coordinate... 0.03 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... sort: invalid option -- 'O'
open: No such file or directory
[bam_sort_core] fail to open file bam
[vfprintf(stdout)] Broken pipe
I´m not sure with what the message "sort: invalid option -- 'O'" is related to. When running the same analysis on the public server, it succesfully produces a BAM file.
Can anyone help me figure out what the problem is?
