Error in mutate() and sort.int()

[sjparkmk]

Hello, I encountered an error while processing my MAGs. The program exited unexpectedly during the dbCAN analysis (R script? housed in comparem2??) step with the errors listed below. Has anyone run into this before?

Table 5: Overview of dbcan cazyme results. Called using run_dbcan.

## Error in `mutate()`:
## ℹ In argument: `substrate_unique = substrate_split %>% unique() %>%
##   sort() %>% list()`.
## Caused by error in `sort.int()`:
## ! 'x' must be atomic

## Error in unique(.): object 'df_dbcan_plot_data' not found

## Error in unique(.): object 'df_dbcan_plot_data' not found

Quitting from lines 73-91 [dbcan-plot-show] (/home/XXX/anaconda3/envs/comparem2/share/comparem2-2.15.1-0/dynamic_report/workflow/scripts/section_dbcan.rmd)

Quitting from lines NA-97 [section_dbcan] (/home/XXX/anaconda3/envs/comparem2/share/comparem2-2.15.1-0/dynamic_report/workflow/scripts/section_dbcan.rmd) Error: ! object 'n_dbcan_substrates' not found Execution halted

[cmkobel]

Thanks for filing a bug

Would you mind attaching the dbcan output (results_comparem2/samples/<sample>/dbcan/dbcan-sub.hmm.out) and the .html report (results_comparem2/report_*.html) ?

[sjparkmk]

Thank you for your reply. I checked the directory, and it seems the dbcan folder is missing. There only locate these folders: "assembly-stats", "benchmarks", "checkm2", "gtdbtk", "mashtree", "report_my_files", "samples", and "visuals".

However, in version files, some messages are as follows.

Maybe you need to run download_eggnog_data.py There was an error retrieving eggnog-mapper DB data: not a valid file "/home/XXX/anaconda3/envs/comparem2/share/comparem2-2.15.1-0/databases/eggnog/eggnog.db" assembly-stats Version: 1.0.1 bakta 1.11.4 CompareM2 v2.15.1 dbcan 4.1.4 pyhdfd78af_1 bioconda emapper-2.1.12 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: unknown / Diamond version found: diamond version 2.1.13 / MMseqs2 version found: 18. 8cc5c / Compatible novel families DB version: 1.0.1 gtdbtk: version 2.4.1 Copyright 2017 Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks InterProScan version 5.59-91.0 Mashtree 1.4.6 seqkit Version: 2.10.1

Should I try to resolve this by running the comparem2 download_eggnog_data.py command? (however, it's not working, right?) My concern is that I have already completed all the database downloads.

Thanks!

[cmkobel]

As dbcan runs per sample, the directory is within samples/

The issue with eggnog (https://github.com/eggnogdb/eggnog-mapper/issues/571) is not relevant for dbcan, as dbcan is entirely independent of the eggnog output.

[sjparkmk]

OK. I understood. However, no any folder related to dbcan is under samples folder.