If you try to use Picard to convert SAM to BAM afterwards you will get this error:
java -Xmx4g -Djava.io.tmpdir=/tmp \
-jar /usr/bin/picard.jar SortSam \
picard.sam.SortSam INPUT=141125_H22TJ_2305_3_L005.sam OUTPUT=141125_H22TJ_2305_3_L005.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
[Sat May 23 01:50:25 PDT 2015] Executing as mpjanic@valkyr on Linux 3.13.0-44-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_79-b14; Picard version: 1.129(b508b2885562a4e932d3a3a60b8ea283b7ec78e2_1424706677) IntelDeflater
Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. length(QUAL) != length(SEQ); File 141125_H22TJ_2305_3_L005.sam; Line 96
Line: ST-E00136:51:H22TJCCXX:5:1101:2502:1783 77 * 0 0 * * 0 0 AATAAACCTCTCCTCCCCGGCGCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
[Sat May 23 01:50:25 PDT 2015] picard.sam.SortSam done. Elapsed time: 0.00 minutes.
So remove -I option from bwa code, and it should be fine.