How do I create Database

[yeoeunyun]

Hi, I gonna create database but I got some problems.

here is my command log.

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rm: cannot remove '/tmp/eMRJikpDGC/gbpln214.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat58.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat58.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt29.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt29.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt35.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt35.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct22.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct22.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat130.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat130.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat52.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat52.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln125.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln125.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat136.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat136.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbenv15.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbenv15.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct93.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct93.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct394.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct394.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon92.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon92.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbenv26.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbenv26.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpri21.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpri21.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam45.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam45.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct393.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct393.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon37.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon37.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon117.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon117.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat186.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat186.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat15.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat15.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon20.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon20.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam50.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam50.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt14.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt14.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln173.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln173.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon175.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon175.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat117.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpat117.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct392.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbbct392.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt42.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt42.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt28.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbvrt28.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon4.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon4.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam49.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam49.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln170.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln170.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln171.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln171.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbrod11.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbrod11.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon118.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon118.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbsyn28.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbsyn28.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon30.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon30.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon143.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon143.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon195.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon195.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon210.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon210.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon137.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbcon137.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam13.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbmam13.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbuna1.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbuna1.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbhtg6.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbhtg6.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln100.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln100.seq.gz.nuc.fna.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln99.seq.gz.aa.faa.zst': No such file or directory
rm: cannot remove '/tmp/eMRJikpDGC/gbpln99.seq.gz.nuc.fna.zst': No such file or directory
Finished building virDmnd.dmnd
Finished building virBbmap
Finished building gbBlastx.dmnd
sh: 1: cannot create /scratch/VirmapDb/Taxonomy.virmap: Permission denied
sh: 1: makeStruct.pl: not found
Finished building taxonomy structure
print() on closed filehandle CS at /home/minsookim/msk/Virmap/virmap-master/DatabaseConstructor/makeVirmapDb.pl line 379.
Finished building all virmap databases

(I just bring a part of the command log because there were too much lines.)

I wonder if this problem is because my system is Ubuntu, not Amazon Linux 2 OR I just missed some steps that you give.

Could you give me any advice?

Thanks in advance Yun

[torptube]

Did you create and mount an SSD filesystem onto /scratch and them set TMPDIR to some location on /scratch?

The installer has only been tested on Amazon Linux 2, and only on a fresh machine. There is code to support Debian, but it's not extensively tested. Regardless, you need to be in an AWS environment and on a machine with an SSD instance store. I would recommend at least 400GB on the instance store.

I haven't tested it on a pre-existing linux system. The install script makes a lot of assumptions on binaries and resources that are pre-installed on an Amazon Linux 2 image.

It also looks line your install isn't complete as not all the scripts installed.

What set of commands did you run to get to this point?

[torptube]

OK, I tested super quickly on a fresh ubuntu system, there was an error in the instruction that told you to set TMPDIR after it was already expected to have been set. I put the instruction in the proper spot.

[yeoeunyun]

Thank you for your response.

I downloaded the files you provided, and followed the steps in README

First, I ran these commands as below, and there were not any problems yet.

chmod 0775 virmapInstall.pl
./virmapInstall.pl

export TMPDIR=/scratch/tmp

But, when I ran this command, we got the problems about dependencies.

makeVirmapDb.pl --outputDir /scratch/VirmapDb

So, I installed some dependencies required in makeVirmapDb.pl and also Virmap.pl.

After that, I ran the Virmap.pl to make sure it was installed properly and there were no problems with it. (I mean I could see the usage)

I tried to create database again, using 'makeVirmapDb.pl', but I got that command log as above, and no files were created.

This is what I'm in right now.

I just wonder that there is the other way to use VirMap in Ubuntu.

Thanks in advance.

Yun

[torptube]

Are you running this on a fresh Ubuntu 18.04 image on AWS?

It looks to me like you may be trying to install this on a pre-existing Ubuntu set up (your username would be "ubuntu' on a vanilla AWS image). That scenario has not been tested and is unlikely to work, as the install script assumes certain AWS environment features and also assumes sudo with no password.

[yeoeunyun]

Okay, I got it.

Thank you for your reply.