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In long documents like the infant gut tutorial, the ToC itself can become very disorienting. It would be great to have some cursor or highlight that indicates where the user's current scrollview is.

Hi, I was trying to download the genome for NCBI using ncbi-genome-download, When I ran the anvi-script-process-genbank-metadata script, I got the genomes, but they are not the same size as those in the database. I wanted to know why there is a difference in size. Can you help?

I came up with a couple of minor outdated stuff in some of the blog pages and wanted to let you know.

For each page, I listed the issues that I came up with: Related lines within the page in quotes and the issue in bold.

1) https://merenlab.org/2019/11/25/visualizing-coverages/

“For this summary we have extensively relied upon this video” (video does not work)
“If you’d like to download the necessary anvi’o files to follow this post, please feel free to download them from here” (link does not work)

Profile DB was outdated, so I migrated it to v37 (tried with both safe and quick modes) but then I got the following issue when I run anvi-interactive:

Config Error: Oh no :( There is a contigs database here at 'CONTIGS.db', but it seems to be
broken :( It is very likely that the process that was trying to create this
database failed, and left behind this unfinished thingy (if you would like to
picture its state you should imagine the baby Voldemort at King's Cross). Well,
anvi'o believes it is best if you make it go away with fire, and try whatever
you were trying before you got this error one more time with a proper contigs
database. End of sad news. Bye now.

2) https://merenlab.org/tutorials/assembly-based-metagenomics/

“If you would like to change something on this page, you can directly edit its source code” (link does not work)

3) https://merenlab.org/tutorials/infant-gut/#chapter-i-genome-resolved-metagenomics

“There is also a step-by-step workflow to describe steps of manual curation here.” (link does not work)
“Centrifuge (code, pre-print) is one of the options to....” (Centrifuge is not a pre-print anymore)
“But once we are done with this, please see the relevant section in this study.” (This is also not a pre-print, link should be updated)

4) https://merenlab.org/2017/06/07/phylogenomics/

“The first thing we need to do is to generate an anvi’o contigs database for each one of them:” (Contigs db for two of the .fa files cannot be created - Salmonella_enterica_21806 and Escherichia_coli_9038. Solved by anvi-script-reformat-fasta Escherichia_coli_9038.fa --seq-type NT -o Escherichia_coli_9038_fixed.fa):

Config Error: Tough. Escherichia_coli_9038_contig_00002_plasmid contains characters that are
not any of A, C, T, G, N, a, c, t, g, n. To save you from later headaches,
anvi'o will not make a database. We recommend you identify what's up with your
sequences. If you want to continue, first reformat the FASTA file (you could use
anvi-script-reformat-fasta with the parameter --seq-type NT, and that would fix
the problem)

5) https://merenlab.org/data/prochlorococcus-metapangenome/

“The URL http://merenlab.org/data/prochlorococcus-metapangenome serves the most up-to-date version of this document.” (URL does not work, the link seems to be wrong)

Color is a subjective thing, especially with the prominence of color blindness in our population. What pops to some may be invisible to others.

So I wanted to ask, does anyone else feel these hyperlinks are difficult to see? On a 1-10 scale of visibility, I would rank these as a 2:

Especially given the visual prominence of our new artifact hyperlinks (green), I fear from my own experience that our hyperlinks are being looked over by readers.

Collection of discrepancies I noticed between the tutorial (after Mete's updates) and my outputs. I'll write one comment per issue as I notice them.

Dear Sir,
Followed the instruction of 'web/_posts/anvio/2017-05-18-working-with-prokka.md' at https://github.com/merenlab/web/blob/master/_posts/anvio/2017-05-18-working-with-prokka.md, and run

 python gff_parser.py prokka/sample.gff --gene-calls gene_calls.txt --annotation gene_annot.txt

I got an error of gff_parser.py which appears in line 43 as:

File "gff_parser.py", line 43, in <module>
    source, version = feature.source.split(':')
ValueError: not enough values to unpack (expected 2, got 1)

Could you please take a look at that? Thank you.