MASURCA error for multiple entries

Question

[kilcdincer]

Hi,

I want to run masurca for 19 entries. However it gives me error like this if I want to run them in single config file. Error is;

" terminate called after throwing instance of 'std::runtime_error'
   what(): CAn't open 'quorum_mer_db.jf' for reading  "

And my config file is;

DATA

PE= a1 500 50 /mnt/14_1.fastq.gz /mnt/14_2.fastq.gz

PE= a2 500 50 /mnt/15_1.fastq.gz /mnt/15_2.fastq.gz

PE= a3 500 50 /mnt/19_1.fastq.gz /mnt/19_2.fastq.gz

PE= a4 500 50 /mnt/21_1.fastq.gz /mnt/21_2.fastq.gz

PE= a5 500 50 /mnt/26_1.fastq.gz /mnt/26_2.fastq.gz
...

END

PARAMETERS

USE_LINKING_MATES = 1

NUM_THREADS = 15

JF_SIZE = 320000000

SOAP_ASSEMBLY=0

END

I tried with other JF size, but again did not work.

Do you know the solution? Thank you

[Kevin Blighe]

Hi, what are the specifications of the machine / environment on which you are running this? Which other JF sizes did you try?

[kilcdincer]

I use remote server. It is ubuntu 16.04 RAM 32 GB, 1TB SSD. I tried 160000000 as other JF size. Since I am trying to assemble candida genomes.

And I tried running MASURCA with the config file with only one genome and I got this error;

"packet_write_wait: Connection to 192.167.78.246 port 22: Broken pipe"

Thanks..

Answer 1

[kilcdincer]

We have used more powerful server and it has worked.

[Kevin Blighe]

Great to hear - thank you.