Tophat problem - IndexError: list index out of range

Jetse · 12-06-2012, 05:54 AM

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?

Jetse · 12-06-2012, 06:03 AM

Solved the problem...

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

enelkinsan · 02-17-2013, 03:02 PM

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 · 02-18-2013, 01:54 AM

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

enelkinsan · 02-18-2013, 05:03 PM

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 · 06-07-2016, 04:53 AM

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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12-06-2012, 06:03 AM	#2
Jetse Member Location: The netherlands Join Date: Nov 2012 Posts: 38	Solved the problem... When you have the same problem, check your arguments on containing a bowtie index...

02-17-2013, 03:02 PM	#3
enelkinsan Member Location: NZ Join Date: May 2012 Posts: 14	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

02-18-2013, 01:54 AM	#4
Jetse Member Location: The netherlands Join Date: Nov 2012 Posts: 38	Does the command ls -l /st_Users/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome*.ebwt return all 6 ebwt files you downloaded?

02-18-2013, 05:03 PM	#5
enelkinsan Member Location: NZ Join Date: May 2012 Posts: 14	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)

06-07-2016, 04:53 AM	#6
nath223 Junior Member Location: U.K. Join Date: Mar 2011 Posts: 2	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?