RefineM

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KeyError in taxon_profile

2

Hi Donovan, I am going through the RefineM pipeline and I encountered an error while performing the gene classification in the taxon_profile script. Command: refinem taxon_profile refinem/called/ refinem/scaffold_stats.tsv /home/whyte/refinem_referencedatabases/gtdb_r95_protein_db.2020-07-30.faa /home/whyte/refinem_referencedatabases/gtdb_r95_taxonomy.2020-07-30.tsv...

estebangongora

ssu_erroneous issue

1

Hi Donovan, Am having an issue with the ssu_erroneous command. The output is given below. What seems o be the issue here? $ refinem ssu_erroneous -x fasta metagenome_test/ taxon_profile_output/ gtdb_r80_ssu_db.2018-01-18.fna/...

Bowenji147

r95 database files for refinem donot contain 16S files?

3

Hey @dparks1134 Just wanted to confirm that r95 GTDB files do not have the 16S files? here-https://data.ace.uq.edu.au/public/misc_downloads/refinem/ Regards Jigyasa

Jigyasa3

RefineM database update

1

Hello, Donovan! I am writing with my old request to update RefineM database according to the new GTDB version. Thanks in advance, Maria

uzunmasha

Installation issues

18

Hello again, I have installed refineM as per instructions, including seperate dependencies, but when I type 'refinem -h' I get the following: Traceback (most recent call last): File "/usr/local/bin/refinem", line...

nixon444

Dear @dparks1134 , I am trying to learn to use refineM as the description of its capacities sound really promising and useful to me. I ran it however, and got...

angelovaag

Inconsistent Nomenclatures of the organisms in r95 and r80 databases

1

Dear Parks, Thanks for providing this awesome RefineM for improving MAGs quality! When using r95 database to assgin taxonomy by protein searching against r95 (r95.faa and r95.taxonomy) and by 16S...

DOieGYuan

refinem ssu_erroneous error

2

when i use this command: **refinem ssu_erroneous -x fasta maxbin3/ taxon_profile_output_dir3/ ~/biosoft/diamond-master/gtdb_r80_ssu_db.2018-01-18.fna ~/biosoft/checkM/RefineM-master/RefineM-master/gtdb_r80_taxonomy.2017-12-15.tsv ssu_output_dir** [2018-10-08 13:35:28] INFO: RefineM v0.0.24 [2018-10-08 13:35:28] INFO: refinem ssu_erroneous -x fasta maxbin3/ taxon_profile_output_dir3/ /home/liu507/biosoft/diamond-master/gtdb_r80_ssu_db.2018-01-18.fna /home/liu507/biosoft/checkM/RefineM-master/RefineM-master/gtdb_r80_taxonomy.2017-12-15.tsv...

zhaohuicheng

I added lines to outliers.py to check whether bin's id match the id in the "outliers" file, e.g., outliers.tsv, taxon_filter.tsv and ssu_erroneous.tsv. it will solve the uncorrectly removing of contigs...

lijierr

Can we use refined and unrefined bins from a sample together?

2

Dear @dparks1134 @kata198 I successfully ran refineM on my samples and obtained filtered bins. But if the starting number of bins in my sample is 20, refineM produces only 1-2...

Jigyasa3