Failed to execute in braker.pl line 2343

[ala98412]

Hi there,

I got the following error message

# Thu May 23 06:25:52 2024:Both protein and RNA-Seq data in input detected. BRAKER will be executed in ETP mode (BRAKER3).
#*********
Use of uninitialized value $2 in concatenation (.) or string at /home/why/Tools/BRAKER-3.0.8/scripts/braker.pl line 2342.
Use of uninitialized value $3 in concatenation (.) or string at /home/why/Tools/BRAKER-3.0.8/scripts/braker.pl line 2342.
awk: cmd. line:1: {print ,}
awk: cmd. line:1:        ^ syntax error
awk: cmd. line:1: {print ,}
awk: cmd. line:1:         ^ syntax error
awk: cmd. line:1: {print ,}
awk: cmd. line:1:          ^ unexpected newline or end of string
Failed to execute: java -version 2>&1 | grep 'openjdk version' | awk -F['"''.'] -v OFS=. '{print ,}' at /home/why/Tools/BRAKER-3.0.8/scripts/braker.pl line 2343.

How do I solve it? Thank you.

Best, Jui-Hung

[xo2003]

Hi,

I also have the same issue as described above while setting --addUTR=on. Since it could be caused by the Java version, I changed the Java version to openjdk version "1.8.0_402". However, it doesn't work at all. My original version is openjdk version "11.0.22" 2024-01-16.

I am also wondering how to solve this issue. Thank you.

[KatharinaHoff]

Please disable UTR prediction.

xo2003 @.***> schrieb am Fr. 31. Mai 2024 um 08:10:

Hi,

I also have the same issue as described above while setting --addUTR=on. Since it could be caused by the Java version, I changed the Java version to openjdk version "1.8.0_402". However, it doesn't work at all. My original version is openjdk version "11.0.22" 2024-01-16.

I am also wondering how to solve this issue. Thank you.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/831#issuecomment-2141296962, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JFH2MVGTIWBYFQM3CTZFAH5XAVCNFSM6AAAAABIE7FYTSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBRGI4TMOJWGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[xo2003]

I reviewed several issues related to training UTR, specifically issues #630 and #638, and got the answers about finding UTR in gene models. Thank you for your reply!

[schloegl]

please try whether this fixes the issue for you

https://github.com/Gaius-Augustus/BRAKER/pull/881

[xo2003]

Which Java OpenJDK version from azul (zulu) would be suitable?

[schloegl]

braker seem to expect java 8

[xo2003]

I encountered the same error in braker.pl at line 2344: $cmdString = "java -version 2>&1 | awk -F['\"''.'] -v OFS=. '/version/ {print $2,$3}'"

I modified line 2344 to $cmdString = "java -version 2>&1 | awk -F '\"' '/version/ {print \$2}'". This change prevented the error message from appearing; however, the program still exits because the Java version does not match 1.8.

GUSHR works well even when the Java version does not meet 1.8. I have tested GUSHR separately with Java 11 and Java 21.

Since the test.sh in GUSHR executed successfully with both Java 11 and Java 21, I commented out lines 2344-2355 in braker.pl to bypass the Java version check. I then ran test6.sh and test7.sh with braker_edited.pl , and it works well when setting JAVA_PATH=/path/to/zulu21.38.21-ca-jdk21.0.5-linux_x64/bin. Here are the log files for test6 [braker_test6.log] and test7 [braker_test7.log].