[hyjkim]

I was able to get tophat running on colorspace reads by doing what many others have mentioned: Removing comment lines in .csfasta and .qual; and converting all -1 qualities to 0.

On 5/8 of my datasets, tophat works great. On the remaining 3 I get the following error.

Traceback (most recent call last):
  File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 2174, in ?
    sys.exit(main())
  File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 2133, in main
    user_supplied_juncs)
  File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1848, in spliced_alignment
    segment_len)
  File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1570, in split_reads
    split_record(read_name, read_seq, read_quals, output_files, offsets, color)
  File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1503, in split_record
    read_seq_temp = convert_color_to_bp(read_seq)
  File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1477, in convert_color_to_bp
    base = decode_dic[base+ch]
KeyError: 'GN'

Has anyone else seen an error like this? Is there a fix available?

[dcjones]

Has anyone else seen an error like this? Is there a fix available?

Yes, I ran into the same thing. I just posted my fix (to the source code) on this thread: http://seqanswers.com/forums/showthread.php?p=26692

[nameeta]

Hi guys,

I'm Daehwan, who made this bug and fixed it, you can grab a fixed version at http://tophat.cbcb.umd.edu/index.html

Thanks

Hi,
I ran tophat-1.1.1 on my single end solid data but I encounter the following error.


Traceback (most recent call last):
File "/mlab/software/tophat-1.1.1.Linux_x86_64/tophat", line 2166, in <module>
sys.exit(main())
File "/mlab/software/tophat-1.1.1.Linux_x86_64/tophat", line 2125, in main
user_supplied_juncs)
File "/mlab/software/tophat-1.1.1.Linux_x86_64/tophat", line 1840, in spliced_alignment
segment_len)
File "/mlab/software/tophat-1.1.1.Linux_x86_64/tophat", line 1562, in split_reads
split_record(read_name, read_seq, read_quals, output_files, offsets, color)
File "/mlab/software/tophat-1.1.1.Linux_x86_64/tophat", line 1495, in split_record
read_seq_temp = convert_color_to_bp(read_seq)
File "/mlab/software/tophat-1.1.1.Linux_x86_64/tophat", line 1469, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: 'CN'

[hyjkim]

Hey Nameeta,

I also get the same types of errors with tophat v1.1.1. I am able to run tophat using v1.1.0 and dcjones' patch. I'd recommend you go that route until tophat fixes the solid-style "." wildcard errors.

[nameeta]

Thanks, I was able to fix it by changing tophat.py and then recompiling.

def convert_color_to_bp(color_seq):
decode_dic = { 'A0':'A', 'A1':'C', 'A2':'G', 'A3':'T', 'A4':'N', 'A.':'N', 'AN':'N',
'C0':'C', 'C1':'A', 'C2':'T', 'C3':'G', 'C4':'N', 'C.':'N', 'CN':'N',
'G0':'G', 'G1':'T', 'G2':'A', 'G3':'C', 'G4':'N', 'G.':'N', 'GN':'N',
'T0':'T', 'T1':'G', 'T2':'C', 'T3':'A', 'T4':'N', 'T.':'N', 'TN':'N',
'N0':'N', 'N1':'N', 'N2':'N', 'N3':'N', 'N4':'N', 'N.':'N', 'NN':'N' }

[yinxiaohe]

Tophat error

I have a problem when I ran tophat with solid colorspace single-end 50bp data . Did anyone has encountered such error ? I have run 5 samples but only the last one get this error. I don't know why , they are the same format data, the only difference is the last one is a little big than the others, about 6G data. Can anyone know the reason and help me to solve this problem? Thank you very much. The error is as follow:
Traceback (most recent call last):
File "/share/disk7-3/wuzhygroup/liwh/tophat/bin/tophat", line 2223, in ?
sys.exit(main())
File "/share/disk7-3/wuzhygroup/liwh/tophat/bin/tophat", line 2181, in main
user_supplied_juncs)
File "/share/disk7-3/wuzhygroup/liwh/tophat/bin/tophat", line 1891, in spliced_alignment
segment_len)
File "/share/disk7-3/wuzhygroup/liwh/tophat/bin/tophat", line 1613, in split_reads
split_record(read_name, read_seq, read_quals, output_files, offsets, color)
File "/share/disk7-3/wuzhygroup/liwh/tophat/bin/tophat", line 1546, in split_record
read_seq_temp = convert_color_to_bp(read_seq)
File "/share/disk7-3/wuzhygroup/liwh/tophat/bin/tophat", line 1520, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: 'GN'

[sameet]

Hello. I can now successfully start and get passed the first error encountered here. However, I still run into the next error mentioned above:

Tue Oct  5 16:10:32 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Tue Oct  5 16:10:32 2010] Preparing output location /home/schaefer/tophat/RBM20/Sample14//
[Tue Oct  5 16:10:32 2010] Checking for Bowtie index files
[Tue Oct  5 16:10:32 2010] Checking for reference FASTA file
[Tue Oct  5 16:10:32 2010] Checking for Bowtie
	Bowtie version:			 0.12.3.0
[Tue Oct  5 16:10:32 2010] Checking for Samtools
	Samtools version:		 0.1.8.0
[Tue Oct  5 16:10:39 2010] Checking reads

Error encountered parsing file ...fastq:
 Length mismatch between sequence and quality strings for 853_8_25/1 (49 vs 49).

When I check the fastq file, everything seems fine:

@853_8_25/1
GNNGTGNTNCANNCGTNNGAGNNCACNNACANCCGANNACGNAAAGNAN
+
*""%%%"%"%%""%%%""%)&""%%%""%%+"&'%&""'(%"'))'"&"
@853_8_35/1
CNNACGNANACNNACCNNCCGNNTAANNNNGNGAACNNCNANCNCNNTN
+
:""=54"@"=+""A98""745"";98""""2"=@>8""<"4"<"6"";"
@853_8_75/1
GNNACCNCNTCNNAACNNTACNNCGANNGTGNGGACNNGTCNCGAGNCN
+
="";<7"0";4""=;:"">;=""94<"".,5".;26""9%)"(%(("("
@853_8_96/1
...

Is this error still occuring to someone else?

I got exact same error. What is worst, I was processing 8 files, I got this error for 5 files but TopHat worked okay for 3 files. This has me completely stumped.

[hrajasim]

I got exact same error. What is worst, I was processing 8 files, I got this error for 5 files but TopHat worked okay for 3 files. This has me completely stumped.

Folks, I am getting exactly the same error for 8 out of 8 FASTQ files that were generated using Casava1.8. BWA aligns everything OK without any compaints.
But TopHat gives me the following:


[Tue Sep 20 16:29:29 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Tue Sep 20 16:29:29 2011] Preparing output location tophat83//
[Tue Sep 20 16:29:29 2011] Checking for Bowtie index files
[Tue Sep 20 16:29:29 2011] Checking for reference FASTA file
[Tue Sep 20 16:29:29 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Sep 20 16:29:29 2011] Checking for Samtools
Samtools Version: 0.1.12a
[Tue Sep 20 16:29:46 2011] Checking reads

Error encountered parsing file ../sample-R32011-083pf.fastq:
Length mismatch between sequence and quality strings for HostName:40:FC:1:1:4494:1059 1:Y:0: (118 vs 192).