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.

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[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!