Java problem

[stien-bckx]

I am running the following command on the university server

shovill --outdir NAZ_bett_assembly --R1 WTCHG_763406_70585034_190687_NAZbett_1.fastq.gz --R2 WTCHG_763406_70585034_190687_NAZbett_2.fastq.gz cpus 10 --ram 64

however, i receive the following error: [shovill] Could not determine version of 'java' via 'java -version 2>&1 | grep version'

If i run the "'java -version 2>&1 | grep version" command, i do not get any errors related to this. Any suggestions on how to solve this?

thanks already

[shovill] Hello stbei [shovill] You ran: /software/shared/apps/x86_64/shovill/1.0.0/bin/shovill --outdir NAZ_bett_assembly --R1 WTCHG_763406_70585034_190687_NAZbett_1.fastq.gz --R2 WTCHG_763406_70585034_190687_NAZbett_2.fastq.gz cpus 10 [shovill] This is shovill 1.0.4 [shovill] Written by Torsten Seemann [shovill] Homepage is https://github.com/tseemann/shovill [shovill] Operating system is linux [shovill] Perl version is v5.28.0 [shovill] Machine has 24 CPU cores and 251.68 GB RAM [shovill] Using bwa - /software/shared/apps/x86_64/bwa/0.7.17/bwa | Version: 0.7.17-r1188 [shovill] Using flash - /software/shared/apps/x86_64/FLASH/1.2.11/flash | FLASH v1.2.11 [shovill] Could not determine version of 'java' via 'java -version 2>&1 | grep version'

[tseemann]

What does java -version say for you?

Can you please upgrade to Shovill 1.1.0 ?

[cabrerad]

Hi! I'm having the same problem as @stien-bckx even though I already upgraded to Shovill 1.1.0.

[shovill] Hello cabrerad [shovill] You ran: /home/cabrerad/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/shovill/bin/shovill --outdir trimmed_Shovill --R1 DRR223365.1_1_val_1.fq --R2 DRR223365.1_2_val_2.fq [shovill] This is shovill 1.1.0 [shovill] Written by Torsten Seemann [shovill] Homepage is https://github.com/tseemann/shovill [shovill] Operating system is linux [shovill] Perl version is v5.32.1 [shovill] Machine has 64 CPU cores and 251.82 GB RAM [shovill] Using bwa - /home/cabrerad/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/shovill/bin/bwa | Version: 0.7.17-r1188 [shovill] Using flash - /home/cabrerad/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/shovill/bin/flash | FLASH v1.2.11 [shovill] Could not determine version of 'java' via 'java -version 2>&1 | grep version'

Do you have any suggestions on how to solve this?

Thank you!