tophat issue-string index out of range

[capricy]

I used tophat to map my RNA seq reads against a reference geneset and it didn't finish.

The error message came after "Generating SAM header":
---------------------------------------------------------
[2013-03-07 10:31:22] Generating SAM header for /gscmnt/gc6108/research/seqana/s
pecies_independant/xgao/a_suum/database/asgenes2
Traceback (most recent call last):
File "/usr/lib/tophat2.0.0/bin/tophat", line 3778, in <module>
sys.exit(main())
File "/usr/lib/tophat2.0.0/bin/tophat", line 3645, in main
params.read_params = check_reads_format(params, reads_list)
File "/usr/lib/tophat2.0.0/bin/tophat", line 1679, in check_reads_format
freader=FastxReader(zf.file, params.read_params.color, zf.fname)
File "/usr/lib/tophat2.0.0/bin/tophat", line 1427, in __init__
while hlines>0 and self.lastline[0] not in "@>" :

IndexError: string index out of range
-------------------------------------------
I am using tophat v2.0.0

I ran 20 sets of data and only one came back with this error message.

Could anyone help me figure out why and how to get over it?

Thanks a lot!

[ttkuaile]

Capricy, I am getting this problem too. Did you ever solve it? if so, any advice on how you did it would be great.

[Artur Jaroszewicz]

Did anyone figure this issue out? The only thing I'm doing differently is I'm using ligated index adaptors and trimming off the first 4 bases from the left reads..

Any input would be greatly appreciated! (Using Tophat 2.0.4)

[ttkuaile]

Artur,
In my case, I got the issue for the trimmed reads with Tophat when I used scythe adapter trimmer (http://biowulf.nih.gov/apps/scythe.html). However, there is no any issue for Tophat when I used another trimmer: http://www.usadellab.org/cms/index.php?page=trimmomatic. So I think the problem is that Tophat can not take your trimmed reads.

[raz]

ttkuaile,
Unfortunately, using the trimmomatic trimmer didn't resolve this issue for me. I'm using tophat version 2.0.8b with bowtie version 2.1.0 on a mac. I'm using the pre-made Arabidopsis indexes from the Bowtie2 site. However I'm ending up with same error (arab is the "index_base" label):

[2013-05-28 22:08:35] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2013-05-28 22:08:35] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-05-28 22:08:35] Checking for Samtools
Samtools version: 0.1.18.0
[2013-05-28 22:08:35] Checking for Bowtie index files
[2013-05-28 22:08:35] Checking for reference FASTA file
[2013-05-28 22:08:35] Generating SAM header for arab
Traceback (most recent call last):
File "/usr/local/bin/tophat-2.0.8b.OSX_x86_64/tophat", line 4030, in <module>
sys.exit(main())
File "/usr/local/bin/tophat-2.0.8b.OSX_x86_64/tophat", line 3885, in main
params.read_params = check_reads_format(params, reads_list)
File "/usr/local/bin/tophat-2.0.8b.OSX_x86_64/tophat", line 1825, in check_reads_format
freader=FastxReader(zf.file, params.read_params.color, zf.fname)
File "/usr/local/bin/tophat-2.0.8b.OSX_x86_64/tophat", line 1570, in __init__
while hlines>0 and self.lastline[0] not in "@>" :
IndexError: string index out of range

I used the following options with the trimmomatic:
phred33
HEADCROP:5 SLIDINGWINDOW:3:30 MINLEN:36


Thanks in advance for the help!

Cheers.

[Marta123]

I had the same error here, and in my case the unpaired output of my trimming program was the problem, because it was not gzip properly (I wrote "sample.gzz"). Fix the name and then all good.
Check the tophat.log that TopHat creates, it normally saids the problem there.

Cheers