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endixk / ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator
http://leb.snu.ac.kr/ezaai
GNU General Public License v3.0
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error for automatic detection of .db files from the directory #12

Closed Ekie22 closed 2 years ago

Ekie22 commented 2 years ago

Hallo, I want to calculate AAI values and use as input just the directory with the profile DBs (db/) as shown in the tutorial

java -jar ~/bin/EzAAI.jar  calculate -i db/ -j db/ -o aai_out/test.tsv

However, I get the following error:

EzAAI - v1.2 [Mar. 2022] java.io.FileNotFoundException: mm.label (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at java.io.FileInputStream.(FileInputStream.java:93) at java.io.FileReader.(FileReader.java:58) at leb.main.EzAAI.runCalculate(EzAAI.java:307) at leb.main.EzAAI.run(EzAAI.java:482) at leb.main.EzAAI.main(EzAAI.java:517)

I also tried it with "db/*.db" but than just the selfcomparison of the first db file is calculated. MMseqs2 Version: 13.45111

Thanks

endixk commented 2 years ago

Hi, would you please run the same command using -dev option and post the full log here?

The command you should run will be:

java -jar ~/bin/EzAAI.jar calculate -i db/ -j db/ -o aai_out/test.tsv -dev

Thanks!

Ekie22 commented 2 years ago

Hi, with the command output I recognized the problem. Within the db/ folder I had a subfolder where I stored db files. It seems that the program tries to use this subfolder: … [MAR 16 08:36:38] DEV |: exec: tar -x -z -f /ezAAI/db/storage [MAR 16 08:36:38] DEV |: exec: /bin/bash -c mmseqs convert2fasta mm /tmp/1a4693815e80be43_faa/i2.faa java.io.FileNotFoundException: mm.label (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at java.io.FileInputStream.(FileInputStream.java:93) at java.io.FileReader.(FileReader.java:58) at leb.main.EzAAI.runCalculate(EzAAI.java:307) at leb.main.EzAAI.run(EzAAI.java:482) at leb.main.EzAAI.main(EzAAI.java:517) [MAR 16 08:36:38] ERROR |: Program terminated with error.

After I moved the subfolder to another location the program ran without trouble. Thanks

endixk commented 2 years ago

Ah yes. Currently the program does not allow any other files/directories to be present within the input directory. I will consider to develop an automated detection feature that can make the program exclusively use the database files only.

Thank you for sharing your experience!