Running 7000+MAGs, no progress after Prodigal

[Burgersnow]

Hello, first of all thank you very much for this very useful tool. I'm having a little trouble reprocessing my data. I had 7000+ MAGs, and after executing commands in the form required by the software, no hmmsearch was performed for 3 days after prodigal ended, and no tmp_run_hmmsearch.sh was generated. It seems the command is stuck somewhere between prodigal and hmmsearch. But when I tested it with 10 MAGs, prodigal immediately followed with hmmsearch. When I used 1600 MAGs tests, it took 5 hours for prodigal to finish running hmmsearch. At this speed, more than 7,000 MAGs could run hmmsearch almost 24 hours after prodigal was completed. I don't know much about perl and wonder if this step between prodigal and hmmsearch takes so long (more than 3 days) when there are a lot of MAGs (7000+MAGs, about 18G in total) to process? Or do you have any other suggestions?

[ChaoLab]

METABOLIC would have problems in processing so many MAGs as we operated it before. Yes, it runs very slow and gets stuck. I will suggest you to run them separately, for example, run 2000 MAGs each time

[Burgersnow]

If I divide these 7000 MAGs into four groups and run the metabolic c.pl program respectively, how can I integrate these four groups of results together to draw metabolic sankey, functional network and other pictures?

[adityabandla]

Running into the same issue with 2000 MAGs

[LvbBo]

If I divide these 7000 MAGs into four groups and run the metabolic c.pl program respectively, how can I integrate these four groups of results together to draw metabolic sankey, functional network and other pictures?

Hi, I encountered the same problem. Have you solved this problem? If so, please tell me the details. Thanks!!!

[Burgersnow]

If I divide these 7000 MAGs into four groups and run the metabolic c.pl program respectively, how can I integrate these four groups of results together to draw metabolic sankey, functional network and other pictures?

Hi, I encountered the same problem. Have you solved this problem? If so, please tell me the details. Thanks!!!

Follow the above suggestion to run in groups of 2000 MAGs each, and finally merge the results.

[LvbBo]

If I divide these 7000 MAGs into four groups and run the metabolic c.pl program respectively, how can I integrate these four groups of results together to draw metabolic sankey, functional network and other pictures?

Hi, I encountered the same problem. Have you solved this problem? If so, please tell me the details. Thanks!!!

Follow the above suggestion to run in groups of 2000 MAGs each, and finally merge the results.

Hi, are you randomly grouping these MAGs? Do these 2000 MAGs come from the same samples? If not, can I group these MAGs randomly? Currently, I have multiple water samples (from the same sea area), divided into several groups (four water layers), each containing different samples. Under such circumstances, how should I use this software? Should I run it four times for the four groups?