@terdon I have already asked a question about it and again I am having the same problem but issue is diiferent.

This is the question bioinformatics.stackexchange.com/questions/4340/…, this issue has been resolved.

But now I am facing another issue that is Root file system has 12 MB space left although root has 3.7T free space available.

@AmmarSabirCheema As I'm sure you understand, I can't help if you just give me a contradictory statement. Ask a question, either here or (probably better from what little you describe) on Unix & Linux, explaining what command tells you you have 12M and what command tells you you have 3.7T

This is usually due to a process keeping a temporary file handle open

@terdon can I share output of df -Th?

please

[dellemc@localhost ~]$ df -Th
Filesystem              Type      Size  Used Avail Use% Mounted on
/dev/mapper/centos-root xfs        50G   44G  6.9G  87% /
devtmpfs                devtmpfs   63G     0   63G   0% /dev
tmpfs                   tmpfs      63G   45M   63G   1% /dev/shm
tmpfs                   tmpfs      63G   20M   63G   1% /run
tmpfs                   tmpfs      63G     0   63G   0% /sys/fs/cgroup
/dev/sda2               xfs      1014M  161M  854M  16% /boot
/dev/sda1               vfat      200M  9.8M  191M   5% /boot/efi

OK, that tells me you have 6.9G available.

But I am running the analysis in home why it is conflicting with root?

and let me share a picture

@AmmarSabirCheema Please ask a question. That way you can give all the necessary information instead of spending a long time asking for each detail. We need to know the command you ran, the directory you ran it in, the output of df you show above, and any other relevant details of your system.

@terdon sorry for late here is the picture if you are not able to answer I can also put it as a question but posting a question for same problem again and again looks absurd

here is the pic that shows I have ran it in which directory imgur.com/a/eeoaMfI

@AmmarSabirCheema It seems like a different problem, why is it the same one? And the reasons it is better to ask a question are: i) other users can also benefit, not just you, but anyone else with the same issue; ii) it is much easier for us to answer because you will give all relevant information instead of me having to ask for every piece and waste your time and mine.

And that image doesn't tell me anything. I am guessing your prompt shows your current directory and so you are in some place called "bilal". But I have no idea where the bilal directory is.

Nor do I know why you think the problem is running out of disk space.

You seem to be allocating 90G of RAM to run this. Do you have that much available?

It is also likely that each of your threads will be allocated 90G of RAM, so you're asking for 90*20=1800GB of RAM

And you seem to have ignored the answers you got before and have now gone back to 20 threads. Why don't you do the same thing you did originally? Lower the threads and ram and try again.

@terdon ok If I did not find any solution I will post a question, you reasons are concrete.

let me run it again and if error comes I will post it

thanks for your useful advice

Thanks. Link back to your origina question, show that you tried running with few threads and less RAM and show the error.

I'm willing to bet that the problem is that each thread is using 90G of RAM though.

@terdon previously the problem was solved using --genomeChrBinNbits and then It gave error for l---limitGenomeGenerateRam

after giving 15 to 1st value and 89 to second and using 15 threads the problem was solved.

great!

Or do you mean the old problem?

old problem

ah

hehe