Hi all,
I am running Tophat/Cufflinks on a RNA-seq datasets(9 samples) from ABI SOLiD. When went through Tophat(v1.1.2), only one sample was terminated with an error message, the rest were doing well and results have already been there.
So it is pretty strange only one sample encountered this error:
[Tue Nov 23 15:14:39 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Tue Nov 23 15:14:39 2010] Preparing output location tophat_SN94.sam.cfasta/
[Tue Nov 23 15:14:39 2010] Checking for Bowtie index files
[Tue Nov 23 15:14:39 2010] Checking for reference FASTA file
[Tue Nov 23 15:14:39 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 23 15:14:39 2010] Checking for Samtools
Samtools version: 0.1.7.0
[Tue Nov 23 15:15:23 2010] Checking reads
min read length: 50bp, max read length: 50bp
format: fasta
[Tue Nov 23 15:30:24 2010] Reading known junctions from GFF file
[Tue Nov 23 15:38:10 2010] Mapping reads against hg19 with Bowtie
[Wed Nov 24 00:51:24 2010] Joining segment hits
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 2201, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 2160, in main
user_supplied_juncs)
File "/usr/local/bin/tophat", line 1870, in spliced_alignment
segment_len)
File "/usr/local/bin/tophat", line 1593, in split_reads
split_record(read_name, read_seq, read_quals, output_files, offsets, color)
File "/usr/local/bin/tophat", line 1526, in split_record
read_seq_temp = convert_color_to_bp(read_seq)
File "/usr/local/bin/tophat", line 1500, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: 'CN'
Has anyone else seen an error like this? Any ideas on what is the reason?
Thanks!
I am running Tophat/Cufflinks on a RNA-seq datasets(9 samples) from ABI SOLiD. When went through Tophat(v1.1.2), only one sample was terminated with an error message, the rest were doing well and results have already been there.
So it is pretty strange only one sample encountered this error:
[Tue Nov 23 15:14:39 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Tue Nov 23 15:14:39 2010] Preparing output location tophat_SN94.sam.cfasta/
[Tue Nov 23 15:14:39 2010] Checking for Bowtie index files
[Tue Nov 23 15:14:39 2010] Checking for reference FASTA file
[Tue Nov 23 15:14:39 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 23 15:14:39 2010] Checking for Samtools
Samtools version: 0.1.7.0
[Tue Nov 23 15:15:23 2010] Checking reads
min read length: 50bp, max read length: 50bp
format: fasta
[Tue Nov 23 15:30:24 2010] Reading known junctions from GFF file
[Tue Nov 23 15:38:10 2010] Mapping reads against hg19 with Bowtie
[Wed Nov 24 00:51:24 2010] Joining segment hits
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 2201, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 2160, in main
user_supplied_juncs)
File "/usr/local/bin/tophat", line 1870, in spliced_alignment
segment_len)
File "/usr/local/bin/tophat", line 1593, in split_reads
split_record(read_name, read_seq, read_quals, output_files, offsets, color)
File "/usr/local/bin/tophat", line 1526, in split_record
read_seq_temp = convert_color_to_bp(read_seq)
File "/usr/local/bin/tophat", line 1500, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: 'CN'
Has anyone else seen an error like this? Any ideas on what is the reason?
Thanks!
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