Hello,
I am running SOAPdn2 on a server and the log file contains the line "aio_return error" some millions of times. The log file is now of 796 GB, mostly these error lines. Above that, the lines are:
Version 2.04: released on July 13th, 2012
Compile Sep 16 2016 15:43:38
********************
Pregraph
********************
Parameters: pregraph -s bart_cfg_file -K 53 -p 20 -R -o bart_53
In bart_cfg_file, 1 lib(s), maximum read length 120, maximum name length 256.
20 thread(s) initialized.
Import reads from file:
/../1.fastq
Import reads from file:
/../2.fastq
--- 100000000th reads.
--- 200000000th reads.
--- 300000000th reads.
--- 400000000th reads.
The server is using all the processors I requested and ~200 Gb of memory, I don't know if it is progressing. It is running like this since about 24 h, for a 400 Mb homozygous genome with some 50-60x of PE data.
The command is SOAPdenovo-63mer all -s bart_cfg_file -p 20 -F -K 53 -R -o bart_53 1>bart_53_ass.log 2>bart_53_ass.err
, the cfg file is
max_rd_len=120
[LIB]
avg_ins=400
reverse_seq=0
asm_flags=3
rd_len_cutoff=120
rank=1
insert size)
pair_num_cutoff=3
least 32 for short insert size)
map_len=32
q1=/1.fastq
q2=/2.fastq
Is it all OK or is there something wrong?
Thanks,
Dario