AAI calculation error
pkstranger opened this issue · 11 comments
I am trying to calculate AAI using EZAAI. I have already created the DB file from genome but when executing command for AAI calculation, programme is terminated in between. Below is the screenshot for same.
$ java -jar EzAAI_latest.jar calculate -i db/ -j db/ -o out/SAOS_164_21_8_21.tsv
[AUG 21 14:09:44] EzAAI |: EzAAI - v1.0 [Mar. 2021]
[AUG 21 14:09:47] EzAAI |: Calculating AAI... [Task 1/1600]
[AUG 21 14:09:59] EzAAI |: Calculating AAI... [Task 2/1600]
[AUG 21 14:10:09] EzAAI |: Calculating AAI... [Task 3/1600]
[AUG 21 14:10:21] EzAAI |: Calculating AAI... [Task 4/1600]
[AUG 21 14:10:32] EzAAI |: Calculating AAI... [Task 5/1600]
[AUG 21 14:10:44] EzAAI |: Calculating AAI... [Task 6/1600]
[AUG 21 14:10:55] EzAAI |: Calculating AAI... [Task 7/1600]
[AUG 21 14:11:05] EzAAI |: Calculating AAI... [Task 8/1600]
[AUG 21 14:11:16] EzAAI |: Calculating AAI... [Task 9/1600]
java.lang.NullPointerException
at leb.process.ProcCalcPairwiseAAI.calcIdentityWithDetails(ProcCalcPairwiseAAI.java:364)
at leb.process.ProcCalcPairwiseAAI.pairwiseMmseqs(ProcCalcPairwiseAAI.java:568)
at leb.process.ProcCalcPairwiseAAI.calculateProteomePairWithDetails(ProcCalcPairwiseAAI.java:243)
at leb.main.EzAAI.runCalculate(EzAAI.java:313)
at leb.main.EzAAI.run(EzAAI.java:445)
at leb.main.EzAAI.main(EzAAI.java:480)
[AUG 21 14:11:26] ERROR |: Program terminated with error.
Hi,
I have the same error as your. Did you solve it?
Hi, I have the same error as your. Did you solve it?
Yes, actually one of my genomes was corrupted. I have redownloaded the sequence and run the command afterward I got the result.
Hi, I also got the same error, how did you find out which genomes were corrupted? did you use prokka .fna files ?
I am trying to calculate AAI using EZAAI. I have already created the DB file from genome but when executing command for AAI calculation, programme is terminated in between. Below is the screenshot for same. $ java -jar EzAAI_latest.jar calculate -i db/ -j db/ -o out/SAOS_164_21_8_21.tsv [AUG 21 14:09:44] EzAAI |: EzAAI - v1.0 [Mar. 2021] [AUG 21 14:09:47] EzAAI |: Calculating AAI... [Task 1/1600] [AUG 21 14:09:59] EzAAI |: Calculating AAI... [Task 2/1600] [AUG 21 14:10:09] EzAAI |: Calculating AAI... [Task 3/1600] [AUG 21 14:10:21] EzAAI |: Calculating AAI... [Task 4/1600] [AUG 21 14:10:32] EzAAI |: Calculating AAI... [Task 5/1600] [AUG 21 14:10:44] EzAAI |: Calculating AAI... [Task 6/1600] [AUG 21 14:10:55] EzAAI |: Calculating AAI... [Task 7/1600] [AUG 21 14:11:05] EzAAI |: Calculating AAI... [Task 8/1600] [AUG 21 14:11:16] EzAAI |: Calculating AAI... [Task 9/1600] java.lang.NullPointerException at leb.process.ProcCalcPairwiseAAI.calcIdentityWithDetails(ProcCalcPairwiseAAI.java:364) at leb.process.ProcCalcPairwiseAAI.pairwiseMmseqs(ProcCalcPairwiseAAI.java:568) at leb.process.ProcCalcPairwiseAAI.calculateProteomePairWithDetails(ProcCalcPairwiseAAI.java:243) at leb.main.EzAAI.runCalculate(EzAAI.java:313) at leb.main.EzAAI.run(EzAAI.java:445) at leb.main.EzAAI.main(EzAAI.java:480) [AUG 21 14:11:26] ERROR |: Program terminated with error.
I had this exact same issue and realized all of the files created from the 'extract' module were corrupted. I thought perhaps it was my sequence files so I downloaded the sample dataset from the EzAAI tutorial and ran the code exactly as it is on the tutorial. All of the .db files are corrupted and I get the same error. This seems to be some type of compatibility issue with EzAAI and certain machines. For reference I am running on MacOS v12.6
Hoping the creators of EzAAI have a suggestion on how to resolve this issue?
Hello @kellikmullane, could you please attach the corrupted .db file from the tutorial set here for us to examine?
@endixk thanks for replying! In order to attach it here, I had to convert it to a .txt file. But I will email you the .db file as well in case the conversion changes something. I ran all of the code exactly the same with the exception that I did not use the -l flag, as I wasn't sure what it did (couldn't find a description of this feature anywhere in the documentation).
Thank you for your swift response! .txt file is broken as expected. I also received the mail but I guess the attachment was removed during the transmission. Could you please upload it as a .zip file by compressing it?
Hopefully this works...
my_example_db.db.zip
Hey Kelli, I examined your DB file and found that the file is modified by SQLite-related program:
$ head my_example_db.db
SQLite format 3@ ���._��������!�P��,L�f�D}"
�4�`*���R
The DB file generated by the extract module is simply a renamed tar.gz file, which should not contain any sort of SQLite metadata. My assumption is that the file has been automatically modified by an external DBMS program, which made the file unrecognizable.
I have the same problem but the extract function made all my genomes unrecognizable, what can I do?