Closed muslih14 closed 6 years ago
In the detailed reports -1 stands for "not in the database". For example: if a certain species is marked with -1 for a specific tool, this species is not available on this tool's database.
By default, metametamerge will just merge species results (parameter ranks
on the configuration file,), so all other ranks (genus and above) will be also marked with -1, since they were just estimated from the species.
Thanks, That makes perfect sense. I've got another question: I'd like to assess the time it takes each tool to process the data, the log and time files seem a bit cyrptic.
Thank you so much for this tool.
You're welcome, I hope the tool is being useful.
Follow the answers:
1 and 2: MetaMeta outputs a log file for each rule inside the pipeline. For the DUDes example, metameta has a rule to align the reads agains the index (dudes_run_1), for the analysis (dudes_run_2) and for converting the tool output to a specified standard (dudes_rpt) that would be parsed by metametamerge.
3: Yes, summing them up will give you the total execution time. You can do that with the following:
cd workdir/sample/log/
grep "^[0-9].*" *.time | cut -f 1 | awk -F ":" '{split($1,t,"_"); sum[t[1]]+=$2}END{for(s in sum) print s, sum[s]}'
4: There is no script to merge the detailed files yet. It should be easily done by reading those files using python and pandas (https://pandas.pydata.org/pandas-docs/stable/merging.html#set-logic-on-the-other-axes). I'll try to add a script for that on the next release.
Cheers, Vitor
It sure is. Thank you, Vitor!
Best wishes, Muslih.
In the final final.metametamerge.profile.out.detailed file. What does the value -1 mean? I understand 0 is absent and between 0 and 1 are the abundance obtained using a specific tool.