Hi Aziz, I can’t give an estimate because it depends on so many things. How
many spectra? Fully tryptic, semi-trypic? How many PTMs? Are you using
Comet? How many cores/threads does your machine have/did you let Comet use?
Etc. If you use Comet, you can usually look at the output to see its
progress. You should see something like:
Search start: 09/29/2020, 10:35:28 AM
- Load spectra: 15009
- Search progress: 29%
- Post analysis: done
- Load spectra: 15009
- Search progress: 54%
Etc.
To get a sense of how quickly progress is being made.
Also, check the RAM usage on your machine to make sure the computer isn’t
swapping due to low memory conditions.
Eric
*From:* [email protected] <[email protected]>
*On Behalf Of *AZIZ ALNAKLI
*Sent:* Wednesday, October 21, 2020 8:45 PM
*To:* [email protected]
*Subject:* Re: [spctools-discuss] maximum fasta file size
Thanks Eric for your reply.
The database I am having is in a single file that is over 10 GB in size. It
has been almost 24 hrs since I got the job run, and it is still running.
Do you have a suggestion on the timeframe of jobs dealing with such huge
files?
Thanks. Regards.
On Thu, Oct 22, 2020 at 3:46 AM 'Eric Deutsch' via spctools-discuss <
[email protected]> wrote:
Hi Aziz, there is no specific maximum size. In general, the larger your
database, the greater the memory requirements and CPU time needed for the
software tools and the lower your sensitivity, although it depends on the
degree of redundancy in your database. Hundreds of MB and hundreds of
thousands of protein sequences is routine.
*From:* [email protected] <[email protected]>
*On Behalf Of *AZIZ ALNAKLI
*Sent:* Tuesday, October 20, 2020 9:15 PM
*To:* [email protected]
*Subject:* [spctools-discuss] maximum fasta file size
Hi
what is the maximum fasta file size that TPP can handle?
Anyone knows?
Thank you all.
--
*Aziz Alnakli*
Master of Research Candidate (Bioinformatics Research Group)
*Faculty of Science and Engineering** | * Level 1 Room 120, F7B Building
(4 Wally's Walk)
Macquarie University, NSW 2109, Australia
*M:* + 61 424375954* | **[email protected]
<[email protected]>*
[image: Image removed by sender. Macquarie University] <http://mq.edu.au/>
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*Aziz Alnakli*
Master of Research Candidate (Bioinformatics Research Group)
*Faculty of Science and Engineering** | * Level 1 Room 120, F7B Building
(4 Wally's Walk)
Macquarie University, NSW 2109, Australia
*M:* + 61 424375954* | **[email protected]
<[email protected]>*
[image: Image removed by sender. Macquarie University] <http://mq.edu.au/>
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