Hello!

Recently I ran the following command:

humann2 --resume --verbose --threads 8 --bypass-translated-search --bypass-prescreen --input ~/miniconda3/envs/humann2/Axenic_30mins_combined.fastq --output ~/miniconda3/envs/humann2/Axenic_30mins_combined_output_2.fastq.gz

I was expecting three .tsv output files; *_genefamilies.tsv, *_pathabundance.tsv and *_pathcoverage.tsv. I only have the Axenic_30mins_combined_genefamilies.tsv file and there is absolutely no sign of the other two? Have I done something wrong, command-wise? What could be the reason for an incomplete set of output files? More importantly, is there a time-efficient way to re-run the command and get those two output files?

If you need any information from the log file to help answer this please let me know. It might be worth noting that at the end of the log file, I see this:

- humann2.utilities - CRITICAL:
CRITICAL ERROR: Unable to process all thread commands.

Error message returned from command for thread task 516: <command>
Error message returned from command for thread task 578: <command>
Error message returned from command for thread task 781: <command>
Error message returned from command for thread task 863: <command>

THANKS IN ADVANCE!

Ahmed