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Just "raw" FASTA files shouldn't be allowed as an artifact. #953
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This seems to be a bigger problem that we initially thought. It turns out that Qiita tries to support this by not passing This pull request adds a more useful error message if a user runs Preprocess without both a fasta and qual file. This illustrates the current issue: $ split_libraries.py -f /Users/caporaso/Dropbox/code/qiita/qiita_core/../qiita_db/support_files/test_data/raw_data/10_seqs.fna -m /tmp/MMF_4bHU5Lp/seqs_MMF.txt -o /tmp/sl_outLlDL5C --barcode_type hamming_8 --max_ambig 6 --max_barcode_errors 1.5 --max_homopolymer 6 --max_primer_mismatch 0 --max_seq_len 1000 --min_qual_score 25 --min_seq_len 200 --qual_score_window 0 --reverse_primer_mismatches 0 --reverse_primers disable
Error in split_libraries.py: To specify a minimum quality score for reads, one must supply quality score files. |
Any luck using a different/new preprocessed parameters set? On Wed, Mar 11, 2015 at 4:25 PM, Greg Caporaso notifications@github.com
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I think that's one solution, but I think that's a bit deeper than I'm able to dive into Qiita at the moment (it sounds like that would have to be a change to the database schema, and that those are challenging to put in place). #972 improves the error message in the meantime. |
Does the act of setting the min qual score value (even to None) force
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Passing any value for On Wed, Mar 11, 2015 at 8:29 PM, Daniel McDonald notifications@github.com
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That's annoying... so ya, even a new set of processed params wouldn't work. On Wed, Mar 11, 2015 at 9:34 PM, Greg Caporaso notifications@github.com
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As a group we decided to not allow just FASTA to be added in to the system as we can't actually use. Renaming the issue. |
We need to change:
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Currently it is only possible to process FASTA studies that include quality files, otherwise you will get a pop-up saying that you need QUAL files.
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