Tophat problem - IndexError: list index out of range

[Jetse]

Hello everyone,

I have a question about tophat like a lot of other people. But this error I couldn't find anywhere on this forum. I'm trying to execute tophat with this command:

/home/sge_share_fedor8/common_scripts/tophat-2.0.6/tophat2 --color --quals --library-type fr-secondstrand -p 1 --bowtie1 -o /home/sge_share_fedor12/jetse/wntSignalling/tophat/nucleimin/run1/nucleimin1aa  /home/sge_share_fedor12/jetse/wntSignalling/rawData/nucleimin/run1/splitted/aasolid0801_20110721_BCPE_LSBetaRNAseq_Nico_NucleiMin_F3.csfasta /home/sge_share_fedor12/jetse/wntSignalling/rawData/nucleimin/run1/splitted/aasolid0801_20110721_BCPE_LSBetaRNAseq_Nico_NucleiMin_F5.csfasta /home/sge_share_fedor12/jetse/wntSignalling/rawData/nucleimin/run1/splitted/aasolid0801_20110721_BCPE_LSBetaRNAseq_Nico_NucleiMin_F3.qual /home/sge_share_fedor12/jetse/wntSignalling/rawData/nucleimin/run1/splitted/aasolid0801_20110721_BCPE_LSBetaRNAseq_Nico_NucleiMin_F5.qual

But when executing tophat, I get this error:

Traceback (most recent call last):
  File "/home/sge_share_fedor8/common_scripts/tophat-2.0.6/tophat", line 4022, in <module>
    sys.exit(main())
  File "/home/sge_share_fedor8/common_scripts/tophat-2.0.6/tophat", line 3799, in main
    right_quals_list = args[4]
IndexError: list index out of range

How can I fix this error?

[Jetse]

Solved the problem...

When you have the same problem, check your arguments on containing a bowtie index...

[enelkinsan]

Hi Jetse,
what did you do to your bowtie index files to solve it? I'm trying to run tophat on the pre-build indexes from the cufflinks page and keep getting the same error


tophat /st_Users/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome /st_Users/Project/Sample_1minus1/S1_minus1.R.1.fastq /st_Users/Project/Sample_1minus1/S1_minus1.R.2.fastq

I've also tried with specifying the path to .gtf with -G option

Will be very thankful, if you reply

Elizabeth

[Jetse]

Does the command ls -l /st_Users/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome*.ebwt return all 6 ebwt files you downloaded?

[enelkinsan]

yes, I've double-checked the indexes path, it is correct
later, I managed to run tophat by choosing bowtie1 option (I think, this one may be versions conflict OR... I don't know. My data is not colourspace)

[nath223]

Hello!

I have the same problem. I could not find or understand how to fix this problem.

tophat -p 6 --color --bowtie1 --quals --library-type fr-secondstrand -G /Genomes/mouce_database_10/mm10_c data1-RNA.csfasta data1-RNA.QV.qual


and this give the error!Traceback (most recent call last):
File "/usr/local/tophat/tophat", line 4095, in <module>
sys.exit(main())
File "/usr/local/tophat/tophat", line 3869, in main
left_quals_list = args[2]
IndexError: list index out of range


I check the location and number of files available in Genome folder. I found 6 .ebwt files in the Genome folder. Was there any other command that could be useful to solve this problem? and what does this error message means?

[paulocress]

An index in Python refers to a position within an ordered list . This error basically means you are trying to access a value at a List index which is out of bounds i.e greater than the last index of the list or less than the least index in the list. So the first element is 0, second is 1, so on. So if there are n elements in a list, the last element is n-1 . If you try to access the empty or None element by pointing available index of the list, then you will get the "List index out of range " error. To solve this error, you should make sure that you're not trying to access a non-existent item in a list.