Tophat Error - What Does This Mean?

Question

[newDNASeqer]

One of my samples failed Tophat and the content of the log is

Traceback (most recent call last): File "/usr/local/bin/tophat-2.0.6/tophat", line 4022, in <module> sys.exit(main()) File "/usr/local/bin/tophat-2.0.6/tophat", line 3782, in main args = params.parse_options(argv) File "/usr/local/bin/tophat-2.0.6/tophat", line 1080, in parse_options self.read_mismatches = int(value) ValueError: invalid literal for int() with base 10: '3--quals'

what does this error mean? any possible fix? thanks

Answer 1

[Peter]

Tophat tried to turn the string '3--quals' into an integer, which failed.

Probably you had an error in your command line (which you didn't show) and there is a missing space in what should have been '3 --quals' in the command.

[newDNASeqer]

I have 32 samples (FastQ) and used the same tophat command, and 31 of them worked successfully. Only one of the samples failed with the above error message. I saw tophat has an option of using '--quals', but I did not set it explicitly in my command. Should I set '3 --quals' explicitly in my command?

[Peter]

What command are you running - it sounds like something in the pipeline could be messing up.

Answer 2

[swbarnes2]

Check your fastq. Maybe there is a glitch in the file, causing there to be wrong characters, and invalid characters in the quality string.