mstubb
commented
8 years ago Hi,
Are you using a version of Igblast newer than 1.4.0. That error message looks like the output format may have changed in the versions that were released this year and so the parser is failing to extract the correct information. If you are using a newer version, the best fix for now will be to download v1.4.0 (ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release//1.4.0) and to see if that works. We’re currently preparing a relatively large update for release and we’ll add support for newer IgBLAST versions in that. In the meantime, if this is the cause, I’ll update the README to emphasise the need to use v1.4.0.
Please let me know if changing IgBLAST version fixes the problem. If it does not, we can investigate further to find out what’s going on.
Best,
Mike
On 29 Jun 2016, at 15:49, prefectus notifications@github.com wrote:
First of all thank you very much for this extremely useful tool. We get an error after the Running IgBLAST part. Independent whether I try the test_data (mouse) or our own data (human):
Running IgBLAST
TCRA
TCRB
Traceback (most recent call last): File "/Seq/tools/tracer/tracer", line 21, in Launcher().launch() File "/Seq/tools/tracer/tracerlib/launcher.py", line 54, in launch getattr(self, args.mode)() File "/Seq/tools/tracer/tracerlib/launcher.py", line 217, in assemble cell = io.parse_IgBLAST(locus_names, output_dir, cell_name, imgt_seq_location, species, seq_method) File "/Seq/tools/tracer/tracerlib/io.py", line 76, in parse_IgBLAST cell = find_possible_alignments(all_locus_data, locus_names, cell_name, IMGT_seqs, output_dir, species, seq_method) File "/Seq/tools/tracer/tracerlib/tracer_func.py", line 103, in find_possible_alignments processed_hit_table = process_hit_table(query_name, query_data, locus) File "/Seq/tools/tracer/tracerlib/tracer_func.py", line 237, in process_hit_table segment = entry[2] IndexError: list index out of range
Do you have any idea what could be wrong? Reagrds, Till
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prefectus
First of all thank you very much for this extremely useful tool. We get an error after the Running IgBLAST part. Independent whether I try the test_data (mouse) or our own data (human):
Running IgBLAST
TCRA
TCRB
Traceback (most recent call last): File "/Seq/tools/tracer/tracer", line 21, in
Launcher().launch()
File "/Seq/tools/tracer/tracerlib/launcher.py", line 54, in launch
getattr(self, args.mode)()
File "/Seq/tools/tracer/tracerlib/launcher.py", line 217, in assemble
cell = io.parse_IgBLAST(locus_names, output_dir, cell_name, imgt_seq_location, species, seq_method)
File "/Seq/tools/tracer/tracerlib/io.py", line 76, in parse_IgBLAST
cell = find_possible_alignments(all_locus_data, locus_names, cell_name, IMGT_seqs, output_dir, species, seq_method)
File "/Seq/tools/tracer/tracerlib/tracer_func.py", line 103, in find_possible_alignments
processed_hit_table = process_hit_table(query_name, query_data, locus)
File "/Seq/tools/tracer/tracerlib/tracer_func.py", line 237, in process_hit_table
segment = entry[2]
IndexError: list index out of range
Do you have any idea what could be wrong? Reagrds, Till