LGliuliuliu
commented
2 years ago Hi,-m 4 format alignment how did you get it
Open Gjocund opened 3 years ago
LGliuliuliu
commented
2 years ago Hi,-m 4 format alignment how did you get it
Hi~
I have tried to run LRScaf using nanopore long reads and an assembly file, and with default parameters in ScafConf.xml. java -jar ~/lrscaf-master/target/LRScaf-1.1.12.jar -x ScafConf.xml The messages I got are similar to this post, https://github.com/shingocat/lrscaf/issues/13:
$ cat logs/error.log 2021-08-26 22:40:34 [ ERROR ] Error: org.apache.commons.cli.MissingArgumentException: The aligned file could not be null! at agis.ps.Main.parsering(Main.java:161) at agis.ps.Main.main(Main.java:48) 2021-08-26 22:40:34 [ ERROR ] agis.ps.Main The aligned file could not be null!
$ cat logs/logs.log 2021-08-26 22:42:23 [ INFO ] Parsing the xml configure, all the other parameters set by command line will dismissed! 2021-08-26 22:42:24 [ INFO ] Launching... 2021-08-26 22:42:24 [ INFO ] Build output folder successfully! 2021-08-26 22:42:24 [ INFO ] Building output folder, elapsed time: 2 ms 2021-08-26 22:43:14 [ INFO ] Reading contigs, elapsed times: 49913 ms 2021-08-26 22:47:51 [ INFO ] Valid Aligned Records: 756966 2021-08-26 22:47:51 [ INFO ] Reading Aligned Records, elapsed time: 277126 ms 2021-08-26 22:47:52 [ INFO ] Finding Repeats: 2021-08-26 22:47:52 [ INFO ] MIN: 1.0 2021-08-26 22:47:52 [ INFO ] First Quartile: 4.0 2021-08-26 22:47:52 [ INFO ] Median cov = 12.0 2021-08-26 22:47:52 [ INFO ] Third Quartile: 17.0 2021-08-26 22:47:52 [ INFO ] MAX: 41645.0 2021-08-26 22:47:52 [ INFO ] Interquartile Range: 13.0 2021-08-26 22:47:52 [ INFO ] 1.5's IQR , Outlier Threshold: 36.5 2021-08-26 22:47:52 [ INFO ] Repeat count: 31624 2021-08-26 22:47:52 [ INFO ] Finding repeat, elapsed time: 528 ms …
Because the error.log said: "Error: The aligned file could not be null!", but the logs.log says, "Valid Aligned Records: 756966", I think these two logs are easy to make first time users confused about how the program is running. I wish the log files could report the real situation (whether the software is doing well), thank you.