Hi
I used bwa before on both 75 mers and 100mers PE reads successfully. However, I have been noticing some issues when I try to run reads that are trimmed off of low quality (residues whose quality correspond to B). The input reads are still paired ends, but the only difference is that they are not of the constant length anymore. Each mate in a pair could be of different sizes (upto 75 mer) based on its quality. BWA ran successfully several times on the same data set before without the quality trimming.
This brings me to the question if bwa can handle inconsistent read lengths during alignment. I also tried to run a small subset of sample reads to check if it finishes successfully, but it fails every time.
The only parameter I am using is n=7. For the larger set it exits saying "User defined signal 2" after trying to process a few million reads while creating the .sai files. I am also pasting the console log for a small subset of trimmed paired end reads I have been trying to run. In either case, it has not even started to write the .sam files.
Any help would be highly appreciated. Thanks!
[bwa_aln_core] calculate SA coordinate... 2016.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 100000 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 3217.48 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 100000 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (58334509, 565854931, 1207105846)
[infer_isize] low and high boundaries: 75 and -2147483648 for estimating avg and std
[infer_isize] inferred external isize from 60 pairs: 632688892.850 +/- 606565808.842
[infer_isize] skewness: 0.710; kurtosis: -0.690
[infer_isize] inferred maximum insert size: -1108636348 (4.21 sigma)
[bwa_sai2sam_pe_core] time elapses: 31.80 sec
[bwa_sai2sam_pe_core] changing coordinates of 22 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
I used bwa before on both 75 mers and 100mers PE reads successfully. However, I have been noticing some issues when I try to run reads that are trimmed off of low quality (residues whose quality correspond to B). The input reads are still paired ends, but the only difference is that they are not of the constant length anymore. Each mate in a pair could be of different sizes (upto 75 mer) based on its quality. BWA ran successfully several times on the same data set before without the quality trimming.
This brings me to the question if bwa can handle inconsistent read lengths during alignment. I also tried to run a small subset of sample reads to check if it finishes successfully, but it fails every time.
The only parameter I am using is n=7. For the larger set it exits saying "User defined signal 2" after trying to process a few million reads while creating the .sai files. I am also pasting the console log for a small subset of trimmed paired end reads I have been trying to run. In either case, it has not even started to write the .sam files.
Any help would be highly appreciated. Thanks!
[bwa_aln_core] calculate SA coordinate... 2016.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 100000 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 3217.48 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 100000 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (58334509, 565854931, 1207105846)
[infer_isize] low and high boundaries: 75 and -2147483648 for estimating avg and std
[infer_isize] inferred external isize from 60 pairs: 632688892.850 +/- 606565808.842
[infer_isize] skewness: 0.710; kurtosis: -0.690
[infer_isize] inferred maximum insert size: -1108636348 (4.21 sigma)
[bwa_sai2sam_pe_core] time elapses: 31.80 sec
[bwa_sai2sam_pe_core] changing coordinates of 22 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
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