aio_return error

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Dario Copetti

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Sep 24, 2016, 1:03:33 AM9/24/16
to BGI-SOAP
1 Q desc. (which area, which software, which version, which env., what error report)

2 Ways I have tried (like searched by google,quora, statckoverflow ...)

3 The point I really hope to know  (what's the mean of * ? how to do  * ?  if it is * ? )


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

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