Originally posted by Papillon
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Since mapping went well with untouched fastq-files, would it be safe for me to assume that tempering with these files can be quite tricky?
The only other cause could be using a newer version of BWA - v. 0.5.9b - and using the -I option for Illumina scoring.
Those are the only differences between being able to map at all and the absolute failures.
In retrospect, this method wasn't powerful enough to begin with, so I removed it from the pipeline.
[bwa_sai2sam_pe_core] time elapses: 10.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 18 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 19395 out of 60331 Q17 singletons are mated.
[bwa_paired_sw] 238 out of 193695 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 22668.70 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.81 sec
[bwa_sai2sam_pe_core] print alignments... 2.02 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (16981, 39972, 70412)
[infer_isize] low and high boundaries: 101 and 177274 for estimating avg and std
[infer_isize] inferred external isize from 39 pairs: 42807.359 +/- 29283.488
[infer_isize] skewness: 0.344; kurtosis: -1.096; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 220265 (6.06 sigma)
[bwa_sai2sam_pe_core] time elapses: 11.07 sec
[bwa_sai2sam_pe_core] changing coordinates of 12 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 20365 out of 59571 Q17 singletons are mated.
[bwa_paired_sw] 253 out of 194428 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 27222.88 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec
[bwa_sai2sam_pe_core] print alignments... 2.03 sec
[bwa_sai2sam_pe_core] 524288 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs
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