meren
commented
3 years ago Thank you for these, @asylvz! I addressed all of them except one, I think:
“If you would like to change something on this page, you can directly edit its source code” (link does not work)
This is coming from a macro, and it will not work for that page :( The entire document needs to be re-written as it extremely narrow minded at this point.
Thank you very much for your diligence and 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I came up with a couple of minor outdated stuff in some of the blog pages and wanted to let you know.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Profile DB was outdated, so I migrated it to v37 (tried with both safe and quick modes) but then I got the following issue when I run anvi-interactive: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)