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Old 06-07-2018, 12:43 PM   #1
fznajar
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Default Blast 2.8.0+

Hi all,
I have been getting the following error:
Error memory mapping:/Volumes/cbbc_expansion1/BLASTDB/nt.43.nnd openedFilesCount=251 threadID=0
BLAST Database error: Error pre-fetching sequence data

I am using version5 pre-formatted nt data. As you can see above, there seem to be a problem with "nt.43".
Any ideas what I am doing wrong.
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Old 06-08-2018, 05:05 AM   #2
Markiyan
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1. Make sure the blast volume #43 is not corrupted, check it's md5 sums.
2. Ensure that your systems has enough RAM available to blast process.
3. Please put your blast db on the DAS (Direct Attached Storage) volume.
(Ideally nvme SSD one with good cooling).

More specifics about the system configuration would be very helpful.
post the outputs from the following commands:
(remove dots from the commands):

l.s.cpu
u.n.ame -a
u.li.mit -a
d.f -h
c.a.t /e.t.c/m.t.ab
t.o.p

Since it is a /Volumes mount point name, I may suspect it is a MacOS system, which probably has 8 or 16GB of RAM, and you would need at least 64 GB for current editions of the nt database.
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Old 06-08-2018, 05:11 AM   #3
GenoMax
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Where did you get blast 2.8.0? Current version available from NCBI's FTP site is v. 2.7.1.
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Old 06-08-2018, 01:41 PM   #4
fznajar
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Thanks a lot Markiyan. You are correct about the 16GB. The checksum is correct.
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Old 06-08-2018, 01:49 PM   #5
fznajar
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GenoMax. Here are the links:

For the executables:
ftp://ftp.ncbi.nlm.nih.gov/blast/exe...t+/2.8.0alpha/

For the new database the goes with it:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/

You would want this version of the database as it allows great features for taxonomy specific blast.
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Old 06-08-2018, 02:14 PM   #6
fznajar
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Here the commands outputs that worked Markiyan

Darwin cbbc.lifesci.nor.ou.edu 16.7.0 Darwin Kernel Version 16.7.0: Tue Jan 30 11:27:06 PST 2018; root:xnu-3789.73.11~1/RELEASE_X86_64 x86_64
----------------------------------

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 256
pipe size (512 bytes, -p) 1
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 709
virtual memory (kbytes, -v) unlimited
---------------------
Filesystem Size Used Avail Capacity iused ifree %iused Mounted on
/dev/disk1 233Gi 189Gi 43Gi 82% 2346076 4292621203 0% /
devfs 196Ki 196Ki 0Bi 100% 678 0 100% /dev
map -hosts 0Bi 0Bi 0Bi 100% 0 0 100% /net
map auto_home 0Bi 0Bi 0Bi 100% 0 0 100% /home
/dev/disk4s2 931Gi 397Gi 534Gi 43% 143983 4294823296 0% /Volumes/cbbc_expansion1
/dev/disk2s1 1.8Ti 1.4Ti 413Gi 78% 4110506 4290856773 0% /Volumes/BACKUP
/dev/disk3s2 3.6Ti 2.2Ti 1.4Ti 62% 1103273 4293864006 0% /Volumes/cbbc_expansion_4TB
-------------------------
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Old 06-09-2018, 03:23 AM   #7
GenoMax
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That is an "alpha" version (meaning a "work in progress") of blast+. I would suggest not using that for any serious work. You should switch to the current shipping version. But as @Markian pointed out with 16G you are not going to have enough RAM to do this search.
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Old 06-09-2018, 04:20 PM   #8
fznajar
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I agree. NCBI released the youtube video explaining how it works. I was impressed with the taxonomy. I am using in house for tests.
I will upgrade the memory of my MacPro soon.
Thanks for your suggestions.
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Old 06-11-2018, 08:47 AM   #9
Markiyan
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A couple of points:

For taxonomy - specific blast it is way better to create a subset(s) of the blast db in the fasta format and format them as a separate databases... - it would help reduce IO and DB size, and should lower RAM requirements.
(Othevice the blast has to look up taxonomy in all nt db volumes on EVERY invocation).

PS:
So yours blast station is a proper mac pro tower? - it may be able to take a general server grade DDR3 ECC reg or DDR2 FBdimm modules (depending on it's age), which can be found at a very reasonable prices on the ebay (compared to the new ones).
But please find first out which types of RAM are compatible with it.

I hope that you are not trying to run it off 1tb portable usb drive in plastic casing, since they may not last long if exposed to heavy IO load.

Also I would think upgrading a system drive to 1TB+ 3D MLC SSD (like samsung 850/860 pro or even NVME (depends on compatibility with your MAC)).
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Old 06-11-2018, 02:47 PM   #10
fznajar
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Thank you Markiyan.
Yes it does take DDR3 ECC RDIMM. Appreciate your suggestions. I thought SSD is not good for continuous heavy IO. Actually, I was planning on the portable 1TB USB drive. Glad you mentioned it.
Thank you.

Last edited by fznajar; 06-11-2018 at 03:54 PM.
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