Closed mchj74 closed 5 years ago
brantfaircloth
commented
5 years ago howdy. what were these assemblies from? and, can you send me the fasta header of 1 or 2? likely that whatever program just updated headers and phyluce needs to know about that.
mchj74
commented
5 years ago howdy.they are from a directory called Trinity-fasta-files yes, here they are:
TRINITY_DN347_c0_g1_i1 len=213 path=[191:0-212] [-1, 191, -2] TRINITY_DN327_c0_g1_i1 len=351 path=[329:0-350] [-1, 329, -2] could you help to fix its problem?
brantfaircloth
commented
5 years ago Can you make sure in $HOME/.phyluce.conf you have:
[headers]
trinity:comp\d+_c\d+_seq\d+|c\d+_g\d+_i\d+|TR\d+\|c\d+_g\d+_i\d+|TRINITY_DN\d+_c\d+_g\d+_i\d+
velvet:node_\d+
abyss:node_\d+
idba:contig-\d+_\d+
spades:NODE_\d+_length_\d+_cov_\d+.\d+This is what currently comes w/ phyluce by default and should be working against the headers that you sent (see last part of the trinity entry, above). If you have something else in the '[header]' section of this file, just delete what's there and enter the above.
mchj74
commented
5 years ago Yes, that fixed the problem!
mchj74
commented
5 years ago Thank you.
Hi Brant. I am trying to use phyluce_assembly_match_contigs_to_probes but it gives the following error:
phyluce_assembly_match_contigs_to_probes --contigs Trinity-fasta-files/ --probes hymenoptera-v2-ANT-SPECIFIC-uce-baits.fasta.txt --output uce-search-results --log-path log
2019-03-29 17:13:22,810 - phyluce_assembly_match_contigs_to_probes - INFO - ======= Starting phyluce_assembly_match_contigs_to_probes ======= 2019-03-29 17:13:22,810 - phyluce_assembly_match_contigs_to_probes - INFO - Version: 1.5.0 2019-03-29 17:13:22,810 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --contigs: /flush3/cha737/testing/Trinity-fasta-files 2019-03-29 17:13:22,810 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --dupefile: None 2019-03-29 17:13:22,810 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --keep_duplicates: None 2019-03-29 17:13:22,810 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --log_path: /flush3/cha737/testing/log 2019-03-29 17:13:22,811 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_coverage: 80 2019-03-29 17:13:22,811 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_identity: 80 2019-03-29 17:13:22,811 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --output: /flush3/cha737/testing/uce-search-results 2019-03-29 17:13:22,811 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --probes: /flush3/cha737/testing/hymenoptera-v2-ANT-SPECIFIC-uce-baits.fasta.txt 2019-03-29 17:13:22,811 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --regex: ^(uce-\d+)(?:_p\d+.*) 2019-03-29 17:13:22,811 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --verbosity: INFO 2019-03-29 17:13:23,042 - phyluce_assembly_match_contigs_to_probes - INFO - Creating the UCE-match database 2019-03-29 17:13:23,091 - phyluce_assembly_match_contigs_to_probes - INFO - Processing contig data 2019-03-29 17:13:23,091 - phyluce_assembly_match_contigs_to_probes - INFO - ----------------------------------------------------------------- Traceback (most recent call last): File "/apps/phyluce/1.6.0/bin/phyluce_assembly_match_contigs_to_probes", line 342, in
main()
File "/apps/phyluce/1.6.0/bin/phyluce_assembly_match_contigs_to_probes", line 291, in main
contig_name = get_contig_name(lz.name1)
File "/apps/phyluce/1.6.0/bin/phyluce_assembly_match_contigs_to_probes", line 229, in get_contig_name
return match.groups()[0]
AttributeError: 'NoneType' object has no attribute 'groups'
It creates the output directory with two files in it, it creates the .trinity.lastz file for the first sample but apparently it gets stuck at some point (do not know where) when trying to match headers. Can you help to fix that issue? tnx