Configuration Info: The endogenous database configuration has been set!
Configuration Info: 37 databases are set!
11:07:45.100 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!
11:07:45.109 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/plug/star/STAR-2.5.3a.zip
11:07:45.569 [main] INFO edu.harvard.channing.compass.utility.Download - Finish to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/plug/star/STAR-2.5.3a.zip
11:07:45.573 [main] ERROR edu.harvard.channing.compass.utility.DeCompress - Fail to uncompress the file /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/plug/star/STAR-2.5.3a.zip
11:07:45.573 [main] ERROR edu.harvard.channing.compass.utility.DeCompress - zip END header not found
11:07:45.573 [main] INFO edu.harvard.channing.compass.utility.Download - File /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/plug/star/STAR-2.5.3a.zip was uncompressed.
11:07:45.573 [main] INFO edu.harvard.channing.compass.core.Produce - ToolKit module was completed.
As I understand COMPSRA is accessing the star zip file and extracting it to ./plugs, as I can then see it there. Then running the alignment example module confirms an issue with running star (STAR not installed correctly):
Configuration Info: The endogenous database configuration has been set!
Configuration Info: 37 databases are set!
11:21:48.482 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!
The hg38 reference genome was set.
QC module will not be performed.
The hg38 was set in default.
Annotation module will not be performed.
Microbe module will not be performed.
Function module will not be performed.
11:21:48.499 [main] ERROR java.lang.Class - STAR was not installed correctly!
Have you any insight on how I can right this? I tried to install STAR v2.5.3a myself per section 2.3 in the COMPSRA manual, however this did not go as planned after extracting 2.5.3a source code to the /bundle_v1/plug directory, and has a similar error culminating in the error above of "STAR was not installed correctly"!
Hi,
Following example, and installing STAR through COMPSRA:
$ java -jar COMPSRA.jar -tk -dr -ck star
+++++++++++++++++++++++++++++++ COMPSRA + (V1.0.2 2020-07-03) + rejia@channing.harvard.edu + +++++++++++++++++++++++++++++++
Working Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3 Bundle Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1 Configuration Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/configuration Plug Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/plug N_CPU: 56
Configuration Info: The endogenous database configuration has been set! Configuration Info: 37 databases are set! 11:07:45.100 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!
+++++++++++++++++++++++++++++++ COMPASS ---> ToolKit + +++++++++++++++++++++++++++++++
11:07:45.109 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/plug/star/STAR-2.5.3a.zip 11:07:45.569 [main] INFO edu.harvard.channing.compass.utility.Download - Finish to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/plug/star/STAR-2.5.3a.zip 11:07:45.573 [main] ERROR edu.harvard.channing.compass.utility.DeCompress - Fail to uncompress the file /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/plug/star/STAR-2.5.3a.zip 11:07:45.573 [main] ERROR edu.harvard.channing.compass.utility.DeCompress - zip END header not found 11:07:45.573 [main] INFO edu.harvard.channing.compass.utility.Download - File /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/plug/star/STAR-2.5.3a.zip was uncompressed. 11:07:45.573 [main] INFO edu.harvard.channing.compass.core.Produce - ToolKit module was completed.
As I understand COMPSRA is accessing the star zip file and extracting it to ./plugs, as I can then see it there. Then running the alignment example module confirms an issue with running star (STAR not installed correctly):
$ java -jar COMPSRA.jar -ref hg38 -aln -mt star -mbi -in ./example_out/sample01/sample01_17to50_FitRead.fastq.gz -out ./example_out/sample01/sample01_17to50_FitRead
+++++++++++++++++++++++++++++++ COMPSRA + (V1.0.2 2020-07-03) + rejia@channing.harvard.edu + +++++++++++++++++++++++++++++++
Working Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3 Bundle Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1 Configuration Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/configuration Plug Directory: /home/usr/COMPSRA/COMPSRA_V1.0.3/bundle_v1/plug N_CPU: 56
Configuration Info: The endogenous database configuration has been set! Configuration Info: 37 databases are set! 11:21:48.482 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!
The hg38 reference genome was set. QC module will not be performed. The hg38 was set in default. Annotation module will not be performed. Microbe module will not be performed. Function module will not be performed.
+++++++++++++++++++++++++++++++ Module ---> Alignment + +++++++++++++++++++++++++++++++
11:21:48.499 [main] ERROR java.lang.Class - STAR was not installed correctly!
Have you any insight on how I can right this? I tried to install STAR v2.5.3a myself per section 2.3 in the COMPSRA manual, however this did not go as planned after extracting 2.5.3a source code to the /bundle_v1/plug directory, and has a similar error culminating in the error above of "STAR was not installed correctly"!
Thanks