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ablab / rnaquast

Quality assessment of de novo transcriptome assemblies from RNA-Seq data
http://cab.spbu.ru/software/rnaquast
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'dict_keys' object is not subscriptable #4

Closed summerXiaHan closed 3 years ago

summerXiaHan commented 4 years ago

Hi, I run rnaQUAST.py successfully several days ago, but now i run with errors no matter how I set the $PYTHONPATH (I had tried for python2.7, python3.5, python3.6). So I install anaconda, and then use conda to create a python3.6 environment, and after i activate the environment, i install rnaQUAST.py and run 'rnaQUAST.py --test' successfully. However, when I try on the real data, error occurs like:

屏幕快照 2020-08-27 下午12 23 11

my command is: rnaQUAST.py --transcripts Bridger.fasta --reference $ref --gtf $gtf -o bridger -t 30 --blat Would you tell me how to deal with it? Thanks!

summerXiaHan commented 4 years ago

rnaQUAST.log

andrewprzh commented 4 years ago

Hi!

That looks like a bug in the new version. Could you try gmap instead of blat in the meantime? (simply remove --blat option).

In general we see that gmap gives more consistent results.

All the best Andrey

andrewprzh commented 4 years ago

Yes, the bug is in general/parallel_blat_run.py at line 84 as indicated: You may change id_transcripts = transcripts_dict.keys()[:] to id_transcripts = list(transcripts_dict.keys())

Bugfix release will be out soon, thanks for reporting!