ERROR: Failed to parse taxonomy file on line 1 [2023-06-15 23:22:45] ERROR: Not a tab-separated line

Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

https://ecogenomics.github.io/GTDBTk/

GNU General Public License v3.0

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ERROR: Failed to parse taxonomy file on line 1 [2023-06-15 23:22:45] ERROR: Not a tab-separated line #524

Closed arijitnus closed 1 year ago

arijitnus commented 1 year ago

Hi, I am running gtdbtk denovo_wf on my Metagenome Assembled Genomes (MAGs) and seems it can't read the taxonomy file from classify_wf. May I seek your opinion on this matter?

I have uploaded the log file and the output classification file

Server information

CPU: Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz
RAM: 131980808 kB

Debugging information

[ ] gtdbtk.log has been included (drag and drop the file to upload).
[ ] Genomes have been included (if possible, and there are few).

gtdbtk.log classification_file.xlsx

pchaumeil commented 1 year ago

Hi,

If you want to read directly the summary files from classify_wf you need to use --gtdbtk_classification_file instead of --custom_taxonomy_file ( although you will have to delete every row where classification is not 7 rank long -i.e all Unclassified Bacteria-)

--custom_taxonomy_file only works with the format GENOME_IDd;p;c;o;f;g;s__, it only has 2 columns.

pchaumeil commented 1 year ago

Ticket closed due to inactivity.