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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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list index out of range error #3

Closed golden75 closed 3 years ago

golden75 commented 4 years ago

Hi I am using rnaQuast 1.5.2 version to run

rnaQUAST.py \ --threads 8 \ --transcripts trinity_K32.Trinity.fasta \ --reference trinity_combine.fasta.transdecoder.cds \ --gtf trinity_combine.fasta.transdecoder.gff3 \ -o output

Hence it is give me this error:

Using non strand specific transcripts...

list index out of range
Traceback (most recent call last):
  File "/isg/shared/apps/rnaQUAST/1.5.2/rnaQUAST.py", line 348, in <module>
    return_code = main_utils()
  File "/isg/shared/apps/rnaQUAST/1.5.2/rnaQUAST.py", line 136, in main_utils
    args.gtf = UtilsAnnotations.clear_gtf_by_reference_chr(args.gtf, ids_chrs, tmp_dir, label_db, logger)
  File "/isg/shared/apps/rnaQUAST/1.5.2/general/UtilsAnnotations.py", line 315, in clear_gtf_by_reference_chr
    gtf_chr = line.strip().split()[0]
IndexError: list index out of range

ERROR! Exception caught!

is there any possible explanation for the error?

andrewprzh commented 4 years ago

Hi, sorry for a delay.

This was a known issue in rnaQUAST and should be fixed since version 1.6. Could you give it a try? v.2.0 can be found here https://github.com/ablab/rnaquast/releases/tag/v.2.0.0 or installed via conda

golden75 commented 4 years ago

Hi, sorry for a delay.

This was a known issue in rnaQUAST and should be fixed since version 1.6. Could you give it a try? v.2.0 can be found here https://github.com/ablab/rnaquast/releases/tag/v.2.0.0 or installed via conda

Thank you very much for the reply. I will have a go at the newer version and will let you know.