Hi all,
I'm getting an error using bwa to align solid reads to hg18.
Here are the steps I have completed, and the error
Create fastq files from my raw solid data (no problems here)
> /bwa-0.5.0/solid2fastq.pl ...
Index my hg18 reference fasta into colour space (no problems)
> /bwa-0.5.0/bwa index -a bwtsw -c human.fasta
Align some small fastq files (500K reads ) (again no problems):
> /bwa-0.5.0/bwa aln -c ./human.fasta read1 > read1.sai
> /bwa-0.5.0/bwa aln -c ./human.fasta read2 > read2.sai
Then sampe the sai files (problems here - I am showing all the output):
> /bwa-0.5.0/bwa sampe human.fasta read1.sai read2.sai read1 read2 out.sam
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: weird pairing
[bwa_sai2sam_pe_core] time elapses: 18.60 sec
[bwa_sai2sam_pe_core] change of coordinates in 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... Segmentation fault
here is a head of the two starting fastq files, in case this will help with debugging:
==> read1 <==
@HS12521_tra19938_4:705_604_1571/2
ATTAAAATTCCAATACTCCACTACCTCGAATTATTCTGTACTAAATTAA
+
,2+262=,*9,95)9123)<2,1/-12,,2//455&+++;#0..*#$&9
@HS12521_tra19938_4:705_604_1602/2
GAGGCCAATCAGAATCAGTTAGAGCCGCTTCAGTCCAAAGACAGGGAAA
+
8<88>9<?99<3>;<<=9;=?67568=7786869;89;8;<&8683&:7
@HS12521_tra19938_4:705_604_1651/2
GCGCAGCTGCTTCGTCTAAAACGAGTAAAAAAAAAGAATGAATAAGGGA
==> read2 <==
@HS12521_tra19938_4:705_604_1571/1
CTATATTGCGGTATAGTAGATAGAACAATTTAACCGAATAGAGGCTTGC
+
A984:;<28<?4&*%*,)222&$214&3&$1;1)%/)(1/79#7++
@HS12521_tra19938_4:705_604_1602/1
GTCGTCTTCCTGATCTACCTTGGGGAAACCAACTCGATCCGCCAACGAC
+
?78>697/=:=95;;<6==8>:=?;><,>;;3359;77;851<7:98,<
@HS12521_tra19938_4:705_604_1651/1
AGTATAAGCTACTTATTTGAGTACAGTGAGCGGGGTAGGCAGTTAAGGA
Does anyone have a suggestion to help me get this working?
I'm getting an error using bwa to align solid reads to hg18.
Here are the steps I have completed, and the error
Create fastq files from my raw solid data (no problems here)
> /bwa-0.5.0/solid2fastq.pl ...
Index my hg18 reference fasta into colour space (no problems)
> /bwa-0.5.0/bwa index -a bwtsw -c human.fasta
Align some small fastq files (500K reads ) (again no problems):
> /bwa-0.5.0/bwa aln -c ./human.fasta read1 > read1.sai
> /bwa-0.5.0/bwa aln -c ./human.fasta read2 > read2.sai
Then sampe the sai files (problems here - I am showing all the output):
> /bwa-0.5.0/bwa sampe human.fasta read1.sai read2.sai read1 read2 out.sam
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: weird pairing
[bwa_sai2sam_pe_core] time elapses: 18.60 sec
[bwa_sai2sam_pe_core] change of coordinates in 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... Segmentation fault
here is a head of the two starting fastq files, in case this will help with debugging:
==> read1 <==
@HS12521_tra19938_4:705_604_1571/2
ATTAAAATTCCAATACTCCACTACCTCGAATTATTCTGTACTAAATTAA
+
,2+262=,*9,95)9123)<2,1/-12,,2//455&+++;#0..*#$&9
@HS12521_tra19938_4:705_604_1602/2
GAGGCCAATCAGAATCAGTTAGAGCCGCTTCAGTCCAAAGACAGGGAAA
+
8<88>9<?99<3>;<<=9;=?67568=7786869;89;8;<&8683&:7
@HS12521_tra19938_4:705_604_1651/2
GCGCAGCTGCTTCGTCTAAAACGAGTAAAAAAAAAGAATGAATAAGGGA
==> read2 <==
@HS12521_tra19938_4:705_604_1571/1
CTATATTGCGGTATAGTAGATAGAACAATTTAACCGAATAGAGGCTTGC
+
A984:;<28<?4&*%*,)222&$214&3&$1;1)%/)(1/79#7++
@HS12521_tra19938_4:705_604_1602/1
GTCGTCTTCCTGATCTACCTTGGGGAAACCAACTCGATCCGCCAACGAC
+
?78>697/=:=95;;<6==8>:=?;><,>;;3359;77;851<7:98,<
@HS12521_tra19938_4:705_604_1651/1
AGTATAAGCTACTTATTTGAGTACAGTGAGCGGGGTAGGCAGTTAAGGA
Does anyone have a suggestion to help me get this working?
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