missing fields in outfile

Question

missing fields in outfile

Closed this issue 3 years ago · 5 comments

Hi Mike,

But the last 3 columns are empty: taxid taxname lineage. They will be important for parsing the contig taxonomy by kingdom, family etc.

From: rule PRIMARY_AA_taxonomy_assignment

Kathie

Answer 1 · 2022-03-04T04:37:23.000Z

You should probably be using the tophits from the secondary output, unless you're talking about the contig annotations as opposed to the seqtable annotations?

Answer 2 · 2022-03-07T15:44:28.000Z

I am talking about contig annotations.

Also, I found that the contigSeqTable.tsv has 14 columns for samples that DON'T have taxonomy, but 19 for those that do:

contigID	seqID	start	stop	len	qual	count	CPM	alnType	taxMethod	kingdom	phylum	class	order	family	genus	species	baltimoreType	baltimoreGroup
contig_1000	169-06-08-13-12_CAGATC:1:140311	11	252	241	17	NA	NA	NA	NA	NA	NA	NA	NA					
contig_1000	120-06-02-24-12_ATCACG:3:171191	214	406	192	0	3	2.989033237	nt	LCA	Viruses	Cressdnaviricota	Arfiviricetes	Cirlivirales	Circoviridae	Circovirus	Circovirus sp.	ssDNA	II

Answer 3 · 2022-03-08T05:12:50.000Z

Hi Kathy,
That issue with the contigSeqTable is fixed in the dev branch and will be in the next release.

The rule PRIMARY_AA_taxonomy_assignment is part of the read-based annotations and it's only real purpose is to find sequences that look like a virus so that they can be analysed in the secondary search. You should take the annotations from the secondary searches. If you look at the secondary AA mmseqs directory, the file MMSEQS_AA_SECONDARY_tophit_aln_sorted should have all the columns.

The direct contig annotations at the moment are a bit simplistic, but those files should be in ASSEMBLY/CONTIG_DICTIONARY/FLYE/results. It's simplistic because it currently only uses the primary nt database, not the secondary nt database.

Answer 4 · 2022-03-08T16:37:30.000Z

Thanks, Mike. This makes sense From: Michael Roach ***@***.***> Date: Monday, March 7, 2022 at 11:13 PM To: shandley/hecatomb ***@***.***> Cc: Mihindukulasuriya, Kathie ***@***.***>, Author ***@***.***> Subject: Re: [shandley/hecatomb] missing fields in outfile (Issue #68) * External Email - Caution * Hi Kathy, That issue with the contigSeqTable is fixed in the dev branch and will be in the next release. The rule PRIMARY_AA_taxonomy_assignment is part of the read-based annotations and it's only real purpose is to find sequences that look like a virus so that they can be analysed in the secondary search. You should take the annotations from the secondary searches. If you look at the secondary AA mmseqs directory, the file MMSEQS_AA_SECONDARY_tophit_aln_sorted should have all the columns. The direct contig annotations at the moment are a bit simplistic, but those files should be in ASSEMBLY/CONTIG_DICTIONARY/FLYE/results. It's simplistic because it currently only uses the primary nt database, not the secondary nt database. — Reply to this email directly, view it on GitHub<#68 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANDVLDN2H42DQVZGPOXN26DU63OVZANCNFSM5P4EN55Q>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

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Answer 5 · 2022-05-23T00:29:40.000Z

Should be fixed in new release