Issues with run-asm-pipeline-post-review.sh Script

[KB Paton]

Hi there,

I am at the final stage of a genome assembly, I have my .review.assembly from Juicebox and am trying to export to fasta by running the script run-asm-pipeline-post-review.sh

I am getting the following error message: 

/path/to/3d-dna/run-asm-pipeline-post-review.sh: line 200: 1 +  / 2100000000 : syntax error: operand expected (error token is "/ 2100000000 ")
/path/to/3d-dna/run-asm-pipeline-post-review.sh: line 201: [: -ne: unary operator expected
:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"
:| Warning: No input for label2 was provided. Default for label2 is ":::debris"
Jul 25, 2024 2:12:03 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Jul 25, 2024 2:12:03 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
Failed to create user directory!
Exception in thread "main" java.lang.ExceptionInInitializerError
at juicebox.tools.HiCTools.main(HiCTools.java:66)
Caused by: java.lang.NullPointerException
at juicebox.DirectoryManager.getHiCDirectory(DirectoryManager.java:113)
at juicebox.HiCGlobals.<clinit>(HiCGlobals.java:52)
... 1 more
Jul 25, 2024 2:12:05 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs.  Unix error code 2.
Jul 25, 2024 2:12:05 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"
:| Warning: No input for label2 was provided. Default for label2 is ":::debris"
tail: invalid number of bytes: ‘+’
tail: invalid number of bytes: ‘+’
tail: invalid number of bytes: ‘+’
tail: invalid number of bytes: ‘+’

....

tail: invalid number of bytes '+' continues for a total of 211 lines

My questions: 

1) it seems like the first two lines are syntax errors in the script. Can I edit the script somehow to fix these? What should I do?

2) what is the meaning of these errors from Java? I have no experience with this language and very little with running Java programs (I know how to edit the heap size and that's about it)

3) What is this long sequence of tail: invalid number of bytes: '+'

Thank you in advance for any advice on this issue!

Kind regards,

Martin

[Olga Dudchenko]

Check the prerequisites to make sure you are running Bash >=4 (and that you are running bash). -Olga

[KB Paton]

Hi, yes, I am running bash 5.0.3

[KB Paton]

Hello, 

Do you have any other suggestions? I am running a suitable version of Bash and the script does not work for me, what can I do?

Thank you,

Martin