I'm running the example code
java -jar rdt-2.5.0-SNAPSHOT-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT and the result looks alright, but unexpectedly it returns non-zero exit code.
Hi,
I'm running the example code
java -jar rdt-2.5.0-SNAPSHOT-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXTand the result looks alright, but unexpectedly it returns non-zero exit code.I see a line with
System.exit(1)here: https://github.com/asad/ReactionDecoder/blob/21b99f8127ba95bde800d2df7fc7d03af9053826/src/main/java/uk/ac/ebi/aamtool/ReactionDecoder.java#L153 Shouldn't it be moved to the end of the catch statement? I believe it should be more appropriate that wayBest, Alexey