No repeats.xml

[MinjieHu]

Hi, I tried to annotate my genome with funannotate(v1.3.3). When I run the test run for the sample data, for all the genomes, it stopped at filtering out bad gene models

[09:32 AM]: now filtering out bad gene models (< 50 aa in length, transposable elements, etc).
Traceback (most recent call last):
  File "/mnt/sequence/mhu2/soft/funannotate-1.3.3/bin/funannotate-predict.py", line 1220, in <module>
    lib.RepeatBlast(EVM_proteins, args.cpus, 1e-10, FUNDB, os.path.join(args.out, 'predict_misc'), Blast_rep_remove)
  File "/mnt/sequence/mhu2/soft/funannotate-1.3.3/lib/library.py", line 3546, in RepeatBlast
    with open(blast_tmp, 'rU') as results:
IOError: [Errno 2] No such file or directory: 'genome3/predict_misc/repeats.xml'

Thanks for the help!

[MinjieHu]

Problem sovled by update diamond from 0.8.22-2 to 0.9.21-1

[nextgenusfs]

Glad you figured out the diamond version problem. Second problem probably tRNAscan installation error. Have a look at the log files which game more information about which commands were run and the errors

[MinjieHu]

It's indeed tRNAscan installation error. It seems that funannotate doesn't check the version tRNAscan. And only when the error turns up, I realized that I didn't install tRNAscan.

[MinjieHu]

By the way, when funannotate try to run interProscan, what file it uses as input? The genome file or the predicted protein file?

[hyphaltip]

It uses the XX.protein.fa file in predict_results folder

On Fri, May 25, 2018 at 8:57 AM ykjyhmj notifications@github.com wrote:

By the way, when funannotate try to run interProscan, what file it uses as input? The genome file or the predicted protein file?

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[nextgenusfs]

Just to add a little bit: if you specify the funannotate output directory as input, it will first look in the update_results folder if it exists, then move onto looking into the predict_results folder. Otherwise it is expecting a protein sequence FASTA file.