Entering edit mode
5.7 years ago
priteshrhsabara
•
0
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.
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.
(2.7 years later) Did you find the answer to this problem?