Question: Kissplice2reftranscriptome error : IndexError
gravatar for jfo
3 days ago by
jfo10 wrote:


I am trying to run the last part of kissplice pipeline, which is kissplice2reftranscriptome and got this error:


kissplice2reftranscriptome -b ORP_corset_all_longest.fasta.transdeco der.bed -k kissplice_out_Fask41_coherents_type_0a.fa -t out_blat_SNP_ORP_ID_80.psl -o mainOutput.tsv -l lowQueryCOverageOutput.tsv


Opening all files and formatting tables...

Collecting data...

Traceback (most recent call last):

File "/home/user/src/anaconda2/bin/kissplice2reftranscriptome", line 4, in <module> __import__('pkg_resources').run_script('kissplice2reftranscriptomelib==1.3.2', 'kissplice2reftranscriptome')

File "/home/user/src/anaconda2/lib/python2.7/site-packages/pkg_resources/", line 748, in run_script self.require(requires)[0].run_script(script_name, ns)

File "/home/user/src/anaconda2/lib/python2.7/site-packages/pkg_resources/", line 1524, in run_script exec(script_code, namespace, namespace)

File "/home/user/src/anaconda2/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 577, in <module> File "/home/usr/src/anaconda2/lib/python2.7/site-packages/kissplice2reftranscriptomelib-1.3.2-py2.7.egg/EGG-INFO/scripts/kissplice2reftranscriptome", line 223, in main

File "build/bdist.linux-x86_64/egg/kissplice2reftranscriptomelib/dataAnalysis/", line 101, in getGeneTable

IndexError: list index out of range

Additional Information:

The only deviation of my analysis from the guide/documentation is that I did not use Trinity for de novo assembly.

Thank you.

kissplice rna-seq snp k2rt • 45 views
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