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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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ERROR! Exception caught! #24

Open woeberdaniela opened 2 weeks ago

woeberdaniela commented 2 weeks ago

Hello! I´m trying to assess the quality of my de novo transcriptome assembly (using Trinity) with rnaQUAST 2.3.0 rnaQUAST.py -c "$trinity_file" -l "$file_left" -r "$file_right" -t 32 $trinity_file is a FASTA file; $file_left and $file_right are forward and reverse reads.

I got the following error message:

Getting reference...

list index out of range
Traceback (most recent call last):
  File "/media/quickdisk/data/miniconda/envs/assembly_control/bin/rnaQUAST.py", line 376, in <module>
    return_code = main_utils(sys.argv)
  File "/media/quickdisk/data/miniconda/envs/assembly_control/bin/rnaQUAST.py", line 100, in main_utils
    reference_dict = UtilsGeneral.list_to_dict(fastaparser.read_fasta(args.reference))
  File "/media/quickdisk/data/miniconda/envs/assembly_control/share/rnaquast-2.3.0-0/general/UtilsGeneral.py", line 106, in list_to_dict
    res[e[0].split()[0].strip()] = e[1].strip()
IndexError: list index out of range

ERROR! Exception caught!

In case you have troubles running rnaQUAST, you can submit the issue to github.com/ablab/rnaquast/issues
Please provide us with rnaQUAST.log file from the output directory.

I´m sorry if it´s an obvious issue, I´m new to transcriptomics and would be glad if someone could help me!

andrewprzh commented 2 weeks ago

Dear @woeberdaniela

Unfortunately, rnaQUAST works only when the reference genome is provided. Also, -l and -r options in rnaQUAST are not for providing left and right reads.

Best Andrey

woeberdaniela commented 2 weeks ago

I understand, thank you for your reply!