Error at STEP 9

[molinfzlvvv]

Hi! Authors

I ran into a problem in STEP 9 where the error showed that it could not infer class for ENST00000672955.ANK2.4, and then it exited the run instead of skipping it.
This was fatal to me, because I was doing the CESAR comparison for a very long time, and I was eager to know the cause and solution of the error and whether I could continue to run from step 9 instead of starting from the beginning, and my run command had added the "--ms" parameter.

Looking forward to your reply. I will appreciate it very much.

Best ragards!

[MichaelHiller]

Is this the only transcript that fails?
And if you run this single job in isolation, is the error repeatable?

@kirilenkobm Could you pls have a look? The error message doesn't mean anything to me.

[molinfzlvvv]

@kirilenkobm @MichaelHiller Hi！authors

I ran into the same problem when I was working on another species of TOGA, and it didn't seem like an accident. I was trying to run a single job, and sorry I couldn't split the correct command line from the pipeline. You can give some suggestions for this problem, I will be appreciated.

Looking forward to your reply.
Best regards !

[MichaelHiller]

OK, it looks like everything works for many transcript but the Mctp2 one crashes.
I have never seen this error before unfortunately.
@kirilenkobm Could you pls have a look? Have you seen this before?

[kirilenkobm]

Hi all, I just pushed a commit to avoid this KeyError.
@molinfzlvvv could you pls somehow get all the logging info about this ENSMUST00000079323.Mctp2.19 transcript? In general, this state should've been unreachable (so, I've never seen that before and simply did not handle it properly).
Could you also pls grep ENSMUST00000079323.Mctp2 from the reference bed file?
Thx

[molinfzlvvv]

Hi, @kirilenkobm
I extracted the contents involved "ENSMUST00000079323. Mctp2" file in the log file and the reference bed file. The file is as follows.
Mctp2.log
Mctp2.txt

It looks like it doesn't seem to have what problem.Please have a look.Or if there was any command line can repeat this step, I don't want to run again, it need a long time.
Thx