Hi,
I'm working now to remap some 1000 genomes exome data with BWA to compare with other exomes I've aligned with BWA. These were originally mapped with Mosaik. I've hit a bit of a snag and I'm checking to see if anyone has also experienced this or has some suggestions on how to fix. Basically, I took the bam file and converted it to the two fastq files (since it's paired end). I then aligned these using BWA aln to the reference (it worked great and fast). However, when I run the sampe step it hits the message below and after that the analysis slows drastically (sam file is only on chromosome 1 after running for two days on a 12 core machine with over 40 Gb of memory). Anyone else seen this?
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (4084, 11785, 30818)
[infer_isize] low and high boundaries: 76 and 84286 for estimating avg and std
[infer_isize] inferred external isize from 207594 pairs: 19383.946 +/- 21062.583
[infer_isize] skewness: 1.370; kurtosis: 0.892; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 148287 (6.12 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.36 sec
[bwa_sai2sam_pe_core] changing coordinates of 385 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[aln_local_core] Potential bug: (155,166) > 65
I'm working now to remap some 1000 genomes exome data with BWA to compare with other exomes I've aligned with BWA. These were originally mapped with Mosaik. I've hit a bit of a snag and I'm checking to see if anyone has also experienced this or has some suggestions on how to fix. Basically, I took the bam file and converted it to the two fastq files (since it's paired end). I then aligned these using BWA aln to the reference (it worked great and fast). However, when I run the sampe step it hits the message below and after that the analysis slows drastically (sam file is only on chromosome 1 after running for two days on a 12 core machine with over 40 Gb of memory). Anyone else seen this?
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (4084, 11785, 30818)
[infer_isize] low and high boundaries: 76 and 84286 for estimating avg and std
[infer_isize] inferred external isize from 207594 pairs: 19383.946 +/- 21062.583
[infer_isize] skewness: 1.370; kurtosis: 0.892; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 148287 (6.12 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.36 sec
[bwa_sai2sam_pe_core] changing coordinates of 385 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[aln_local_core] Potential bug: (155,166) > 65
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