Hi,
I am running bwa 0.5.9 on a custom, indexed, sequence database comprised of various genbank sequences.
When I run:
bwa aln gb.fa x_1.fq > a.sai
bwa aln gb.fa x_2.fq > b.sai
bwa sampe gb.fa a.sai b.sai x_1.fq x_2.fq > gb.sam
bwa crashes on bwa sampe with:
[bns_restore_core] fail to open file ' VirtualSequence=""></div><div id="viewercontent13" class="seq gbff" val="381286149" SequenceSize="29462" VirtualSequence=""></div><div id="viewercontent14" class="seq gbff" val="381283770" SequenceSize="35021" VirtualSequence=""></div><div id="viewercontent15" class="seq gbff" val="381286161" SequenceSize="29364" VirtualSequence=""></div><div id="viewercontent16" class="seq gbff" val="381282985" SequenceSize="9499" VirtualSequence=""></div><div id="viewercontent17" class="seq gbff" val="381216220" SequenceSize="16093" VirtualSequence=""></div><div id="viewercontent18" class="seq gbff" val="381147283" SequenceSize="5929" VirtualSequence=""></div><div id="viewercontent19" class="seq gbff" val="380307325" SequenceSize="10631" VirtualSequence=""></div><div id="viewercontent20" class="seq gbff" val="380862749" SequenceSize="6588" VirtualSequence=""></div>'. Abort!
./test.sh: line 3: 25171 Aborted bwa sampe gb.fa a.sai b.sai x_1.fq x_2.fq > gb.sam
The 9GB gb.fa database file was indexed with default, as per the instructions provided and no errors were returned from the indexing.
When I run the same sets of bwa commands using a different, human genome database, there are no errors.
I was wondering whether characters others than ACGTN in the seq. db would make bwa sampe crash (there are such characters in the gb.fa)? Has anyone seen an error like this?
Thanks for your help
Rene
I am running bwa 0.5.9 on a custom, indexed, sequence database comprised of various genbank sequences.
When I run:
bwa aln gb.fa x_1.fq > a.sai
bwa aln gb.fa x_2.fq > b.sai
bwa sampe gb.fa a.sai b.sai x_1.fq x_2.fq > gb.sam
bwa crashes on bwa sampe with:
[bns_restore_core] fail to open file ' VirtualSequence=""></div><div id="viewercontent13" class="seq gbff" val="381286149" SequenceSize="29462" VirtualSequence=""></div><div id="viewercontent14" class="seq gbff" val="381283770" SequenceSize="35021" VirtualSequence=""></div><div id="viewercontent15" class="seq gbff" val="381286161" SequenceSize="29364" VirtualSequence=""></div><div id="viewercontent16" class="seq gbff" val="381282985" SequenceSize="9499" VirtualSequence=""></div><div id="viewercontent17" class="seq gbff" val="381216220" SequenceSize="16093" VirtualSequence=""></div><div id="viewercontent18" class="seq gbff" val="381147283" SequenceSize="5929" VirtualSequence=""></div><div id="viewercontent19" class="seq gbff" val="380307325" SequenceSize="10631" VirtualSequence=""></div><div id="viewercontent20" class="seq gbff" val="380862749" SequenceSize="6588" VirtualSequence=""></div>'. Abort!
./test.sh: line 3: 25171 Aborted bwa sampe gb.fa a.sai b.sai x_1.fq x_2.fq > gb.sam
The 9GB gb.fa database file was indexed with default, as per the instructions provided and no errors were returned from the indexing.
When I run the same sets of bwa commands using a different, human genome database, there are no errors.
I was wondering whether characters others than ACGTN in the seq. db would make bwa sampe crash (there are such characters in the gb.fa)? Has anyone seen an error like this?
Thanks for your help
Rene
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