convert_color_to_bp in Tophat still problematic
I have installed the patch posted by dcjones on , but when running Tophat on SOLiD colorspace paired-end read data I seem to have uncovered another problem with convert_color_to_bp:
tophat -C -F 0.10 -p 12 --mate-inner-dist 125 --mate-std-dev 25 --microexon-search --GFF ucsc-genes-with-GRCh-IDs.gtf GRCh37-lite_c test_F3.csfasta test_F5-P2.csfasta
[Fri Oct 8 15:15:19 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Fri Oct 8 15:15:19 2010] Preparing output location ./tophat_out/
[Fri Oct 8 15:15:19 2010] Checking for Bowtie index files
[Fri Oct 8 15:15:19 2010] Checking for reference FASTA file
[Fri Oct 8 15:15:19 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Oct 8 15:15:19 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Fri Oct 8 15:15:35 2010] Checking reads
min read length: 25bp, max read length: 50bp
format: fasta
[Fri Oct 8 17:05:10 2010] Reading known junctions from GFF file
[Fri Oct 8 18:01:36 2010] Mapping reads against GRCh37-lite_c with Bowtie
[Fri Oct 8 23:30:08 2010] Joining segment hits
[Sat Oct 9 04:14:44 2010] Mapping reads against GRCh37-lite_c with Bowtie(1/2)
[Sat Oct 9 08:28:21 2010] Mapping reads against GRCh37-lite_c with Bowtie(2/2)
[Sat Oct 9 12:59:31 2010] Mapping reads against GRCh37-lite_c with Bowtie
[Sun Oct 10 00:08:07 2010] Joining segment hits
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 2174, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 2133, in main
user_supplied_juncs)
File "/usr/local/bin/tophat", line 1848, in spliced_alignment
segment_len)
File "/usr/local/bin/tophat", line 1570, in split_reads
split_record(read_name, read_seq, read_quals, output_files, offsets, color)
File "/usr/local/bin/tophat", line 1503, in split_record
read_seq_temp = convert_color_to_bp(read_seq)
File "/usr/local/bin/tophat", line 1477, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: '+1'
make: *** [tophat_out/accepted_hits.sam] Error 1
I have installed the patch posted by dcjones on , but when running Tophat on SOLiD colorspace paired-end read data I seem to have uncovered another problem with convert_color_to_bp:
tophat -C -F 0.10 -p 12 --mate-inner-dist 125 --mate-std-dev 25 --microexon-search --GFF ucsc-genes-with-GRCh-IDs.gtf GRCh37-lite_c test_F3.csfasta test_F5-P2.csfasta
[Fri Oct 8 15:15:19 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Fri Oct 8 15:15:19 2010] Preparing output location ./tophat_out/
[Fri Oct 8 15:15:19 2010] Checking for Bowtie index files
[Fri Oct 8 15:15:19 2010] Checking for reference FASTA file
[Fri Oct 8 15:15:19 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Oct 8 15:15:19 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Fri Oct 8 15:15:35 2010] Checking reads
min read length: 25bp, max read length: 50bp
format: fasta
[Fri Oct 8 17:05:10 2010] Reading known junctions from GFF file
[Fri Oct 8 18:01:36 2010] Mapping reads against GRCh37-lite_c with Bowtie
[Fri Oct 8 23:30:08 2010] Joining segment hits
[Sat Oct 9 04:14:44 2010] Mapping reads against GRCh37-lite_c with Bowtie(1/2)
[Sat Oct 9 08:28:21 2010] Mapping reads against GRCh37-lite_c with Bowtie(2/2)
[Sat Oct 9 12:59:31 2010] Mapping reads against GRCh37-lite_c with Bowtie
[Sun Oct 10 00:08:07 2010] Joining segment hits
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 2174, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 2133, in main
user_supplied_juncs)
File "/usr/local/bin/tophat", line 1848, in spliced_alignment
segment_len)
File "/usr/local/bin/tophat", line 1570, in split_reads
split_record(read_name, read_seq, read_quals, output_files, offsets, color)
File "/usr/local/bin/tophat", line 1503, in split_record
read_seq_temp = convert_color_to_bp(read_seq)
File "/usr/local/bin/tophat", line 1477, in convert_color_to_bp
base = decode_dic[base+ch]
KeyError: '+1'
make: *** [tophat_out/accepted_hits.sam] Error 1
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