Problems with TopHat v1.4.0

[luigra]

Dear all I'm trying to use the last version of tophat (v1.4.0) by using the -GTF flag (the reads are mapped before on transcripts). What exactly I'm running is:

tophat --output-dir=<$Output_dir> --mate-inner-dist=30 --mate-std-dev=20 --min-anchor-length=5 --num-threads=8 --closure-search --keep-tmp --GTF=<$transcriptome_file> --transcriptome-index=<$Out_index> <$Index_File> <$R1_Fast> <$R2_Fast>

Obviously the $ items are replaced by the real names

The programs seems to work for more than nine hours but after the point "Searching for junctions via segment mapping" it stopped with the following error:

Traceback (most recent call last):
File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3063, in ?
sys.exit(main())
File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3029, in main
user_supplied_deletions)
File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 2681, in spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers


am I doing something wrong or alternatively it is a program problem?

Thanks in advance
luigi

[fgh1124]

I also met this problem

I also met this problem. Waiting for senior guys give some suggestion.

[fgh1124]

Dear all I'm trying to use the last version of tophat (v1.4.0) by using the -GTF flag (the reads are mapped before on transcripts). What exactly I'm running is:

tophat --output-dir=<$Output_dir> --mate-inner-dist=30 --mate-std-dev=20 --min-anchor-length=5 --num-threads=8 --closure-search --keep-tmp --GTF=<$transcriptome_file> --transcriptome-index=<$Out_index> <$Index_File> <$R1_Fast> <$R2_Fast>

Obviously the $ items are replaced by the real names

The programs seems to work for more than nine hours but after the point "Searching for junctions via segment mapping" it stopped with the following error:

Traceback (most recent call last):
File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3063, in ?
sys.exit(main())
File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3029, in main
user_supplied_deletions)
File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 2681, in spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers


am I doing something wrong or alternatively it is a program problem?

Thanks in advance
luigi

if you do not use "--closure-search", The result is OK!