sinamajidian
commented
3 months ago Hello It would be great if you could share with us a few things: the command line you ran, how you generated marker genes, the mplog.log file and the output log on screen when you ran read2tree.
I think you ran it a few times, which makes it difficult to debug. Read2tree tries to resume previous runs using log and output folder. Please start over in a empty folder if it doesnt take too much resource.
pengyan19
Hi, when i used the read2tree, i meet a question as follows:
Re-loading files: 5997 OGs [02:42, 36.81 OGs/s] Re-loading references for mapping from folder: 100%|?????| 5/5 [00:00<00:00, 7.16 species/s] Loading alignments : 0 Alignment [00:00, ? Alignment/s] Mapping reads to species: 0%| | 0/5 [00:00<?, ? species/s]/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/subprocess.py:961: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdout = io.open(c2pread, 'rb', bufsize) /public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/subprocess.py:966: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) No match found for '[MAIN] Done (', found '[' (at char 0), (line:1, col:1) Mapping reads to species: 0%| | 0/5 [00:00<?, ? species/s] Traceback (most recent call last): File "/public/home/pengyan/biosoft/read2tree/read2tree/bin/read2tree", line 16, in
main(sys.argv[1:], exe_name=exe_name(), desc=desc)
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/main.py", line 357, in main
mapper = Mapper(args, og_set=ogset.ogs, ref_set=reference.ref, progress=progress) # Run the mapping
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 80, in init
self._map_reads_to_references(ref_set)
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 289, in _map_reads_to_references
processed_reads = self._call_wrapper(ref_tmp_file_handle, reads,
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 110, in _call_wrapper
ngm = ngm_wrapper()
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/wrappers/read_mappers/ngm.py", line 62, in call
self.result = self._read_result(error, self.ref_input, self.tmp_folder)
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/wrappers/read_mappers/ngm.py", line 117, in _read_result
result = parser.to_dict(outfile, output)
File "/public/home/pengyan/anaconda3/envs/r2t/lib/python3.10/site-packages/read2tree/wrappers/read_mappers/parser.py", line 43, in to_dict
reads_mapped, total_reads, mapping_time = self.parse(stdout)
TypeError: cannot unpack non-iterable NoneType object