error in compare.py of CNCI package
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Entering edit mode
2.7 years ago

Hi,

I am currently working on lncRNA using CNCI package. I have identified more than 10,000 coordinates of probable lncRNA using cufflinks-cuffcompare, based on class-codes and now I want to identified coding non-coding potential of it. When I am trying to run compare.py command of CNCI package, I am facing following error.

Classification start:
Input genes:  8004
Running Cuffcompare ...
Classifying based on Cuffcompare results:
Known coding genes: 0
Known lincRNA genes: 281
Undefinable genes: 686
Potentially novel genes: 7037
Genes missing classification by cuffcompare: 0
Saving gtf files ...
Traceback (most recent call last):
  File "compare.py", line 272, in <module>
    all_info=Table.paste(gene_class,[1],known_coding,[1],known_noncoding,[1],overlap_coding,[1],overlap_noncoding,[1])
  File "/home/orf8/Desktop/CNCI-master/Table.py", line 908, in paste
    value_cols=sub_array(range(1,len(A.data[0])+1),key_cols)
IndexError: list index out of range

Though it generate some statistics files in cuffcompare folder of cnci_out which noncoding_stat file shows as follow.

Summary for dataset: cnci_1_out/cuffcompare/combined.gtf :
#     Query mRNAs :   10630 in    8158 loci  (0 multi-exon transcripts)
#            (0 multi-transcript loci, ~1.3 transcripts per locus)
# Reference mRNAs :    4645 in    4545 loci  (0 multi-exon)
# Super-loci w/ reference transcripts:      399
#--------------------|   Sn   |  Sp   |  fSn |  fSp  
        Base level:       0.6     5.5     -       - 
        Exon level:       0.2     0.1     0.2     0.1
      Intron level:       -       -       -       -  
Intron chain level:       -       -       -       -  
  Transcript level:       0.0     0.0     0.0     0.0
       Locus level:       0.0     0.0     0.0     0.0

     Matching intron chains:       0
              Matching loci:       0

          Missed exons:    4238/4645    ( 91.2%)
           Novel exons:   10004/10630   ( 94.1%)
           Missed loci:    4146/4545    ( 91.2%)
            Novel loci:    7664/8158    ( 93.9%)

 Total union super-loci across all input datasets: 8063

Can anyone explain about error and how can I solve it to run next-step of CNCI?

Thank you.

RNA-Seq next-gen software error • 811 views
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Entering edit mode

That looks like an "internal" error of that script, and I expect the developers to understand best what's going on. Have you tried contacting them?

However, I also found this unresolved issue which seems to describe the same problem, unanswered for half a year.

This looks like a classic example of people abandoning academic software as soon as it's published.

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Entering edit mode

(2.7 years later) Did you find the answer to this problem?

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