Hi,
I am running SOAPdenovo2 with 1 set of paired-end and 1 set mate pair reads, fragments of 300bp with a total to 66X coverage on a genome with estimated 240Mb.
The sparse_pregraph module on SOAPdenovo2 launched more than 4 days ago and it showed the message below. When I do top it shows in sleeping mode what suggests it could be either reading the reads or writing something but I am concerned it is taking far too long with no verbose on the terminal.
Any one with experience with SOAPdenovo2 maybe can let me know whether it is normal that it takes this long...
$ ./SOAPdenovo-127mer sparse_pregraph -s file.config -K 127 -z 240000000 -o pregraph -p 64
Version 2.04: released on July 13th, 2012
Compile Apr 9 2014 15:54:20
********************
SparsePregraph
********************
Parameters: pregraph_sparse -s file.config -K 127 -g 15 -z 240000000 -d 1 -e 1 -r 0 -p 64 -o pregraph
Start to build the sparse de Brujin graph, round: 1
1 io thread initialized.
Import reads from file:
reads/pe_A520-R1.fastq
64 work threads initialized.
...still showing only this on terminal
$ top
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
44528 x 20 0 9158m 4.4g 1208 S 2419.8 0.9 166092:11 SOAPdenovo-127m
I am running SOAPdenovo2 with 1 set of paired-end and 1 set mate pair reads, fragments of 300bp with a total to 66X coverage on a genome with estimated 240Mb.
The sparse_pregraph module on SOAPdenovo2 launched more than 4 days ago and it showed the message below. When I do top it shows in sleeping mode what suggests it could be either reading the reads or writing something but I am concerned it is taking far too long with no verbose on the terminal.
Any one with experience with SOAPdenovo2 maybe can let me know whether it is normal that it takes this long...
$ ./SOAPdenovo-127mer sparse_pregraph -s file.config -K 127 -z 240000000 -o pregraph -p 64
Version 2.04: released on July 13th, 2012
Compile Apr 9 2014 15:54:20
********************
SparsePregraph
********************
Parameters: pregraph_sparse -s file.config -K 127 -g 15 -z 240000000 -d 1 -e 1 -r 0 -p 64 -o pregraph
Start to build the sparse de Brujin graph, round: 1
1 io thread initialized.
Import reads from file:
reads/pe_A520-R1.fastq
64 work threads initialized.
...still showing only this on terminal
$ top
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
44528 x 20 0 9158m 4.4g 1208 S 2419.8 0.9 166092:11 SOAPdenovo-127m
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