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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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error with "phyluce_align_get_only_loci_with_min_taxa" #310

Closed Gefsy closed 6 months ago

Gefsy commented 10 months ago

Hi all, when i run"phyluce_align_get_align_summary_data ", I got summary as 2023-08-24 23:30:53,548 - phyluce_align_get_align_summary_data - INFO - [Matrix 50%] 1466 alignments 2023-08-24 23:30:53,548 - phyluce_align_get_align_summary_data - INFO - [Matrix 55%] 1036 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 60%] 782 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 65%] 570 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 70%] 309 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 75%] 188 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 80%] 115 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 85%] 45 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 90%] 23 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 95%] 8 alignments

But when I went to get the 50p alignment, I just got "423 alignments" and some error as 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - ======= Starting phyluce_align_get_only_loci_with_min_taxa ====== 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Version: 1.7.1 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Commit: None 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --alignments: /home/dell/data/Gerridae/UCE/taxon-sets/all/mafft-nexus-internal-trimmed-gblocks-clean 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --cores: 12 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --input_format: nexus 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --log_path: /home/dell/data/Gerridae/UCE/taxon-sets/all/log 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --output: /home/dell/data/Gerridae/UCE/taxon-sets/all/mafft-nexus-internal-trimmed-gblocks-clean-50p 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --percent: 0.5 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --taxa: 91 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --verbosity: INFO 2023-08-24 23:28:46,257 - phyluce_align_get_only_loci_with_min_taxa - INFO - Getting alignment files --- Logging error --- Traceback (most recent call last): File "/home/dell/miniconda3/envs/phyluce-1.7.1/lib/python3.6/logging/init.py", line 996, in emit stream.write(msg) UnicodeEncodeError: 'ascii' codec can't encode character '\u2265' in position 132: ordinal not in range(128) Call stack: File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 128, in main() File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 119, in main sum(results), len(results), args.percent, min_count Message: 'Copied 423 alignments of 2681 total containing \u2265 0.5 proportion of taxa (n = 45)' Arguments: () --- Logging error --- Traceback (most recent call last): File "/home/dell/miniconda3/envs/phyluce-1.7.1/lib/python3.6/logging/init.py", line 996, in emit stream.write(msg) UnicodeEncodeError: 'ascii' codec can't encode character '\u2265' in position 124: ordinal not in range(128) Call stack: File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/Hi all, when i run"phyluce_align_get_align_summary_data ", I got summary as 2023-08-24 23:30:53,548 - phyluce_align_get_align_summary_data - INFO - [Matrix 50%] 1466 alignments 2023-08-24 23:30:53,548 - phyluce_align_get_align_summary_data - INFO - [Matrix 55%] 1036 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 60%] 782 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 65%] 570 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 70%] 309 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 75%] 188 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 80%] 115 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 85%] 45 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 90%] 23 alignments 2023-08-24 23:30:53,549 - phyluce_align_get_align_summary_data - INFO - [Matrix 95%] 8 alignments

But when I went to get the 50p alignment, I just got "423 alignments" and some error as 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - ======= Starting phyluce_align_get_only_loci_with_min_taxa ====== 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Version: 1.7.1 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Commit: None 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --alignments: /home/dell/data/Gerridae/UCE/taxon-sets/all/mafft-nexus-internal-trimmed-gblocks-clean 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --cores: 12 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --input_format: nexus 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --log_path: /home/dell/data/Gerridae/UCE/taxon-sets/all/log 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --output: /home/dell/data/Gerridae/UCE/taxon-sets/all/mafft-nexus-internal-trimmed-gblocks-clean-50p 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --percent: 0.5 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --taxa: 91 2023-08-24 23:28:46,256 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --verbosity: INFO 2023-08-24 23:28:46,257 - phyluce_align_get_only_loci_with_min_taxa - INFO - Getting alignment files --- Logging error --- Traceback (most recent call last): File "/home/dell/miniconda3/envs/phyluce-1.7.1/lib/python3.6/logging/init.py", line 996, in emit stream.write(msg) UnicodeEncodeError: 'ascii' codec can't encode character '\u2265' in position 132: ordinal not in range(128) Call stack: File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 128, in main() File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 119, in main sum(results), len(results), args.percent, min_count Message: 'Copied 423 alignments of 2681 total containing \u2265 0.5 proportion of taxa (n = 45)' Arguments: () --- Logging error --- Traceback (most recent call last): File "/home/dell/miniconda3/envs/phyluce-1.7.1/lib/python3.6/logging/init.py", line 996, in emit stream.write(msg) UnicodeEncodeError: 'ascii' codec can't encode character '\u2265' in position 124: ordinal not in range(128) Call stack: File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 128, in main() File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 119, in main sum(results), len(results), args.percent, min_count Message: 'Copied 423 alignments of 2681 total containing \u2265 0.5 proportion of taxa (n = 45)' Arguments: () 2023-08-24 23:28:46,679 - phyluce_align_get_only_loci_with_min_taxa - INFO - ====== Completed phyluce_align_get_only_loci_with_min_taxa ======

I want to know why the numbers of alignments can't mach the summary, and how i fix the error. I'd greatly appreciate any help anyone can offer! main() File "/home/dell/miniconda3/envs/phyluce-1.7.1/bin/phyluce_align_get_only_loci_with_min_taxa", line 119, in main sum(results), len(results), args.percent, min_count Message: 'Copied 423 alignments of 2681 total containing \u2265 0.5 proportion of taxa (n = 45)' Arguments: () 2023-08-24 23:28:46,679 - phyluce_align_get_only_loci_with_min_taxa - INFO - ====== Completed phyluce_align_get_only_loci_with_min_taxa ======

I want to know why the numbers of alignments can't mach the summary, and how i fix the error. I'd greatly appreciate any help anyone can offer!

brantfaircloth commented 9 months ago

There is probably some mismatch in the number of taxa you are inputting (91) versus the number of taxa that are really in the alignments. It is hard to say without additional information (e.g. the total output from the summary command).

Gefsy commented 9 months ago

After aligned and trimmmed the loci, the summary showed the max taxon was 67 (93 taxon input at first). And when i used the "phyluce_align_get_only_loci_with_min_taxa ", if input --taxa 67, i could get the same number as summary(eg:[Matrix 60%]814 alignments); but if input --taxa 93, i could just get alignments less than 100. As the tutorial, taxa is the total number of organisms in the study (eg :93), but I can't solve the above problem. Thank you a lots! ---------- Alignment summary ----------------------- phyluce_align_get_align_summary_data - INFO - [Alignments] loci: 2,683 phyluce_align_get_align_summary_data - INFO - [Alignments] length: 236,786 phyluce_align_get_align_summary_data - INFO - [Alignments] mean: 88.25 phyluce_align_get_align_summary_data - INFO - [Alignments] 95% CI: 0.87 phyluce_align_get_align_summary_data - INFO - [Alignments] min: 25 phyluce_align_get_align_summary_data - INFO - [Alignments] max: 296 ------------------- Informative Sites summary ------------------- phyluce_align_get_align_summary_data - INFO - [Sites] loci: 2,683 phyluce_align_get_align_summary_data - INFO - [Sites] total: 94,177 phyluce_align_get_align_summary_data - INFO - [Sites] mean: 35.10 phyluce_align_get_align_summary_data - INFO - [Sites] 95% CI: 0.39 phyluce_align_get_align_summary_data - INFO - [Sites] min: 0 phyluce_align_get_align_summary_data - INFO - [Sites] max: 85 ------------------------- Taxon summary ------------------------- phyluce_align_get_align_summary_data - INFO - [Taxa] mean: 33.90 phyluce_align_get_align_summary_data - INFO - [Taxa] 95% CI: 0.42 phyluce_align_get_align_summary_data - INFO - [Taxa] min: 3 phyluce_align_get_align_summary_data - INFO - [Taxa] max: 67 --- Data matrix completeness summary --------------- phyluce_align_get_align_summary_data - INFO - [Matrix 50%] 1508 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 55%] 1075 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 60%] 814 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 65%] 591 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 70%] 327 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 75%] 199 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 80%] 120 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 85%] 45 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 90%] 26 alignments phyluce_align_get_align_summary_data - INFO - [Matrix 95%] 11 alignments