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Old 12-06-2012, 04:54 AM   #1
Jetse
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Thumbs down Tophat problem - IndexError: list index out of range

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:
Code:
/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:
Code:
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?

Last edited by Jetse; 12-07-2012 at 01:19 AM. Reason: Fixed
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Old 12-06-2012, 05:03 AM   #2
Jetse
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Solved the problem...

When you have the same problem, check your arguments on containing a bowtie index...
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Old 02-17-2013, 02:02 PM   #3
enelkinsan
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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
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Old 02-18-2013, 12:54 AM   #4
Jetse
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Does the command ls -l /st_Users/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome*.ebwt return all 6 ebwt files you downloaded?
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Old 02-18-2013, 04:03 PM   #5
enelkinsan
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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)
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Old 06-07-2016, 03:53 AM   #6
nath223
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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?
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