query name missing in TopHat2 output bam

Question

[wowee]

Hi, all:

I got a problem with the TopHat2 output accepted.bam(TopHat v2.0.9).

Most of them were normal, while some query name were missing, like following:

    89  chr5    3505612 50  150M    *   0   0   TCCAACGGCACCCTGCACCACTACTTCGTCCCCGACGGGGACTACGAGGAGAACGACGACCCCGAACGCTGCCAGCTGCTCTTCAGGGTGCGCGAGCAGCGGCGGTGCGGCACGGCGGCAGCGGGCGAAGGGCTGAGCCTGCGGGAGGAN  -<FFA--))7JF7--AF<-AJ<7FF---7-JF-----JJFJAJFJJ<--FJJJJJJFJ7JJJ<<JJJJJAFJJJAJJJF-FJFJAFJJJ7-A<<-FJJAJJJJJJJJJJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFA<A#  AS:i:-4 XN:i:XM:i:2 XO:i:0  XG:i:0  NM:i:2  MD:Z:90A58G0    YT:Z:UU XS:A:+  NH:i:1
E00515:57:HCNHYALXX:6:1101:14955:1661   419 chr5    57480591    3   150M    =   57480690    249 TGAGCCCGCCGGATCGCTTGAGCCCAGGAGTTCTGGGCTGCAGTGCGCTATGCCGAGCGGGCGTCCGCGCTAAGGCCGGCATCAATATGGTGAGCCCCGGGGAGCCGAGGCACACCAGGTTGCCTAAGGAGGGGTGAACAGGCCCAGGTC  AAAFFJJJFFJFJJFJJ-FJFJJJJJJJJJFF<AFJJJJ<FFJJF-7JFJ<JFAJJJJJJJFJF-7A7<A-AFFJAF77AJFJJJJJJJJJFAJ--7FFJAA-AFFF-A7AA<FFFJJ))7AA777AFJ-77)-)-)AF-<F7)-)<)<7  AS:i:-3 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:139C10 YT:Z:UU NH:i:2  CC:Z:=  CP:i:57585959HI:i:0

Can anyone help me to understand why this happened?

Thank you.

[IP]

Are you viewing the file in the terminal?

[wowee]

yes, and I doubted that these qurey name were duplicated in the input fastq file, but I found these were unique.

[GenoMax]

At a minimum update TopHat to the latest version (v.2.1.1). You are using software that was current in mid-2013.

TopHat is deprecated at this time and should really be replaced with a newer aligner. If you prefer a suite like tuxedo than use HISAT2/StringTie from developers of TopHat.

[wowee]

Thanks, I will try your suggestions.