extract mitchonderial genome from NGS reads about 90 GB

[Mariamdar]

I tried to run the MitoZ tool on 90GB of DNA data to extract the reads belonging to mitochondrial DNA and construct the genome. I ran it on the server, but I kept getting the same error that I couldn't detect. here the log file
mitoz.log

[linzhi2013]

This command failed:

megahit  --out-dir ./megahit_out  --num-cpu-threads 16 --k-list 59,79,99 --memory 1500000000000.0 -1 /home/ubuntu/Idmi_reference/clean_data/Idmi.clean_R1.fq.gz -2 /home/ubuntu/Idmi_reference/clean_data/Idmi.clean_R2.fq.gz

perhaps your server ran out of memory?

[Mariamdar]

When i used 300 gb memery was the same , should i reduce the number of kmers?

[linzhi2013]

I do not remember if the "megahit" directory has the log from the megahit command, you may check it first; and you should also check the stderr file from mitoz (the 'mitoz.log' only has the stdout).

Otherwise, you can try this command directly and see what will happen (check the stderr and stdout):

megahit  --out-dir ./megahit_out  --num-cpu-threads 16 --k-list 59,79,99 --memory 1500000000000.0 -1 /home/ubuntu/Idmi_reference/clean_data/Idmi.clean_R1.fq.gz -2 /home/ubuntu/Idmi_reference/clean_data/Idmi.clean_R2.fq.gz

Do you know how much memory your server has? The program would fail if it only has 50 GB and you specified 300 GB.

[Mariamdar]

yes i run the code and here the error

[linzhi2013]

yes i run the code and here the error

thanks for the post.

The last line says that you are running out of disk space on your machine

You may have to delete some unneeded files or add a new disk.

[Mariamdar]

Can i delete the parameter of -memory to let the tool working on the space that it is need it ? Or put -memory free?
because i working on server

[linzhi2013]

computer memory and disk space are different things.

your current problem is there is not enough disk space on your server, which can not be solved by using the -memory parameter.