hi Coach, I met with this issue: FATAL: while extracting /home/lyhe/.singularity/cache/oci-tmp/7ddae9be99ba04db37484ae3ac2f99a02f6c03bf79b214a6f1d5336dacae4763: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled. How can I solve this, please
I still having an serious issue concerning the execution of the files. I've downloaded the db using docker and run as it is in the tutorial. I running at a local machine with 6x12 cpu and 16 gb memory, and even using -c 4, ulimit -n 8192. I still got the same error with ...open pages issues....
I suspect the ulimit is not set permantly. The settings vary across different linux system. So I will suggest you look up how it is set permanently in your Operating system
@@bioinformaticscoach Hi! I've tried to set by adjusting in both ulimit, and in the file inside the system. Although I see that limit set is above 8000, by using ulimit -S and -H. I still got the same error messages. I believe that it might be an issue with docker OR with my ubuntu distro.
@@carloscosta3608 try the command ulimit -n and see what number comes up. If the number is less than 8192 then it means your configuration had no effect. Try to look up how it is set for your linux distro. Also if you think docker is given you an issue you can try singularity. That is what I used in this tutorial
Dear Coach, Which files did I can to use to be submitted to NCBI? And, What kind of program do you suggest evaluating of a bacterial genome assembly and annotation?
Can you make your question clearer? Lets put it this way, what do you want achieve at the end of the study? Once you know the answer, it will be easier for suggestions to be made.
@@bioinformaticscoach Sorry. My aim is to submit bacterial genomes, and my question is What kind of programs do you suggest evaluating a bacterial genome assembly and annotation? Thanks in advance!
hi Coach, I met with this issue: FATAL: while extracting /home/lyhe/.singularity/cache/oci-tmp/7ddae9be99ba04db37484ae3ac2f99a02f6c03bf79b214a6f1d5336dacae4763: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled. How can I solve this, please
Hi, can you do a video on how to setup singularity. Finding it difficult.
Hello. Thank you for the video. How to set the installing directory instead of $HOME/dir?
Great
hi Coach, I met with this issue: FATAL: while extracting /home/lyhe/.singularity/cache/oci-tmp/7ddae9be99ba04db37484ae3ac2f99a02f6c03bf79b214a6f1d5336dacae4763: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled. How can I solve this, please
I still having an serious issue concerning the execution of the files. I've downloaded the db using docker and run as it is in the tutorial. I running at a local machine with 6x12 cpu and 16 gb memory, and even using -c 4, ulimit -n 8192. I still got the same error with ...open pages issues....
I suspect the ulimit is not set permantly. The settings vary across different linux system. So I will suggest you look up how it is set permanently in your Operating system
@@bioinformaticscoach Hi! I've tried to set by adjusting in both ulimit, and in the file inside the system. Although I see that limit set is above 8000, by using ulimit -S and -H. I still got the same error messages. I believe that it might be an issue with docker OR with my ubuntu distro.
@@carloscosta3608 try the command ulimit -n and see what number comes up. If the number is less than 8192 then it means your configuration had no effect. Try to look up how it is set for your linux distro.
Also if you think docker is given you an issue you can try singularity. That is what I used in this tutorial
Dear Coach, Which files did I can to use to be submitted to NCBI? And, What kind of program do you suggest evaluating of a bacterial genome assembly and annotation?
Can you make your question clearer? Lets put it this way, what do you want achieve at the end of the study? Once you know the answer, it will be easier for suggestions to be made.
@@bioinformaticscoach Sorry. My aim is to submit bacterial genomes, and my question is What kind of programs do you suggest evaluating a bacterial genome assembly and annotation? Thanks in advance!
@@ManuelRamirez-dr1sk You can use tool called QUAST to evaluate the assembly.
If it is novel genus than how to make Submol.yaml file
This question can be best answered by the developers. Please post here : github.com/ncbi/pgap
Great
hi Coach, I met with this issue: FATAL: while extracting /home/lyhe/.singularity/cache/oci-tmp/7ddae9be99ba04db37484ae3ac2f99a02f6c03bf79b214a6f1d5336dacae4763: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled. How can I solve this, please