Just "raw" FASTA files shouldn't be allowed as an artifact.

[ElDeveloper]

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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.

[gregcaporaso]

This seems to be a bigger problem that we initially thought. It turns out that Qiita tries to support this by not passing -q and -d if there are no qual files provided, but --min_qual_score 25 also needs to be excluded from the command in this case.

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.

[wasade]

Any luck using a different/new preprocessed parameters set?

On Wed, Mar 11, 2015 at 4:25 PM, Greg Caporaso [email protected] wrote:

This seems to be a bigger problem that we initially thought. It turns out that Qiita tries to support this by not passing -q and -d if there are no qual files provided, but --min_qual_score 25 also needs to be excluded from the command in this case.

This pull request adds a more useful error message if a user runs Preprocess without both a fasta and qual file.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78386129.

[gregcaporaso]

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.

[wasade]

Does the act of setting the min qual score value (even to None) force split_libraries to need qual? On Mar 11, 2015 7:47 PM, "Greg Caporaso" [email protected] wrote:

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 https://github.com/biocore/qiita/pull/972 improves the error message in the meantime.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78409607.

[gregcaporaso]

Passing any value for --min_qual_score makes -q required. I don't think passing None would parse as the option parser expects an int.

On Wed, Mar 11, 2015 at 8:29 PM, Daniel McDonald [email protected] wrote:

Does the act of setting the min qual score value (even to None) force split_libraries to need qual? On Mar 11, 2015 7:47 PM, "Greg Caporaso" [email protected] wrote:

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 https://github.com/biocore/qiita/pull/972 improves the error message in the meantime.

Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78409607.

Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78417861.

[wasade]

That's annoying... so ya, even a new set of processed params wouldn't work. It actually would be a small fix to make split_libraries handle this but that would necessitate 1.9.1 and that would not be fun

On Wed, Mar 11, 2015 at 9:34 PM, Greg Caporaso [email protected] wrote:

Passing any value for --min_qual_score makes -q required. I don't think passing None would parse as the option parser expects an int.

On Wed, Mar 11, 2015 at 8:29 PM, Daniel McDonald <[email protected]

wrote:

Does the act of setting the min qual score value (even to None) force split_libraries to need qual? On Mar 11, 2015 7:47 PM, "Greg Caporaso" [email protected] wrote:

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 https://github.com/biocore/qiita/pull/972 improves the error message in the meantime.

Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78409607.

Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78417861.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/953#issuecomment-78418292.

[antgonza]

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.

[antgonza]

We need to change:

• [ ] code and configuration of plugins
• [ ] code in Qiita
• [ ] documentation in Qiita
• [ ] perhaps the upload configuration