SEA-PHAGES | Problem BLASTING after PECAAN file transferred to DNA Master

Link to this post \| posted 16 May, 2020 03:18
byrumc@cofc.edu	I have been trying for several days to make the final DNA Master file after transferring the PECAAN txt file into the DNA Master Documentation section (on my Mac). I've tried to do this at least 7 times. First, I uploaded the FASTA file into DNA Master and then BLASTed all. After trying this twice I was able to get a file that had the BLAST results in it. I then went to the documents page in DNA Master and replaced that info with the PECAAN full annotation text file info (I selected all and replaced…I'm on my Mac, so I can't right click). That went well, but after adding the PECAAN info and parsing, all of my BLAST info disappeared. I cleared all BLAST data (just in case any was left)…and BLASTED again…it puts in the requests, but usually 0 results are read (sometimes it gets to 1 or 4 results read, but usually says 0 results read). It says Too many outstanding requests, attempting to retrieve results before initiating more queries. The the window disappears and there is nothing in the DNA Master file. All of the PECAAN info is gone, all of the predicted genes are gone and there is no BLAST information. I've been working on this for the last 2 days…trying slightly different approaches and the same thing keeps happening. I've never had this problem in the past. Is it because there are so many trying to submit their genomes right now and BLAST is overloaded? I've run the program at peak and non-peak hours. Any suggestions? Thanks for your help! Christine

Link to this post | posted 16 May, 2020 03:18

I have been trying for several days to make the final DNA Master file after transferring the PECAAN txt file into the DNA Master Documentation section (on my Mac). I've tried to do this at least 7 times.

First, I uploaded the FASTA file into DNA Master and then BLASTed all. After trying this twice I was able to get a file that had the BLAST results in it. I then went to the documents page in DNA Master and replaced that info with the PECAAN full annotation text file info (I selected all and replaced…I'm on my Mac, so I can't right click). That went well, but after adding the PECAAN info and parsing, all of my BLAST info disappeared. I cleared all BLAST data (just in case any was left)…and BLASTED again…it puts in the requests, but usually 0 results are read (sometimes it gets to 1 or 4 results read, but usually says 0 results read). It says Too many outstanding requests, attempting to retrieve results before initiating more queries. The the window disappears and there is nothing in the DNA Master file. All of the PECAAN info is gone, all of the predicted genes are gone and there is no BLAST information.

I've been working on this for the last 2 days…trying slightly different approaches and the same thing keeps happening. I've never had this problem in the past. Is it because there are so many trying to submit their genomes right now and BLAST is overloaded? I've run the program at peak and non-peak hours.

Any suggestions? Thanks for your help!

Christine

Link to this post \| posted 16 May, 2020 18:39
cdshaffer	NCBI is quite restrictive in running BLAST searches that are submitted by computer programs like DNA Master and not submitted by individuals using the web interface. NCBI is really just not able to keep up with all the blast searches everyone around the world wants and so these automatically submitted searches are getting more and more restrictive. Your BLAST searches at NCBI do not stop if you quit DNA Master, so every time you retry the searches you add more and more searches to your queue and there is a limit to how many searches you can do at any one time. Given you have tried 7 times this is probably why you are getting this "Too many outstanding requests" error. According to the DNA Master settings it will submit 25 searches at a time so you may have submitted up to 175 searches if DNA master really did submit 25 searches each of those 7 times. According to the rules on this page: "We will move searches of users who submit more than 100 searches in a 24 hour period to a slower queue, or, in extreme cases, will block the requests. " Given that you used PECAAN all the blast results are available to any one who is checking your annotations, so i would suggest you go ahead and submit your DNA Master file without redoing the BLAST results and just note in the cover sheet the issues you had with NCBI and that the BLAST results are available in PECAAN.

Link to this post | posted 16 May, 2020 18:39

cdshaffer

NCBI is quite restrictive in running BLAST searches that are submitted by computer programs like DNA Master and not submitted by individuals using the web interface. NCBI is really just not able to keep up with all the blast searches everyone around the world wants and so these automatically submitted searches are getting more and more restrictive. Your BLAST searches at NCBI do not stop if you quit DNA Master, so every time you retry the searches you add more and more searches to your queue and there is a limit to how many searches you can do at any one time. Given you have tried 7 times this is probably why you are getting this "Too many outstanding requests" error. According to the DNA Master settings it will submit 25 searches at a time so you may have submitted up to 175 searches if DNA master really did submit 25 searches each of those 7 times.

According to the rules on this page: "We will move searches of users who submit more than 100 searches in a 24 hour period to a slower queue, or, in extreme cases, will block the requests. "

Given that you used PECAAN all the blast results are available to any one who is checking your annotations, so i would suggest you go ahead and submit your DNA Master file without redoing the BLAST results and just note in the cover sheet the issues you had with NCBI and that the BLAST results are available in PECAAN.

Link to this post \| posted 16 May, 2020 22:13
byrumc@cofc.edu	Thanks so much for the feedback! That helps. I BLASTED again yesterday (before I got your note) and let it go all night, but it froze again. I closed that and then tried again this morning (Saturday…maybe there was less traffic). It took 9 hours, but it finally worked! Whew! I didn't know that the BLAST searches would continue after I quit DNA Master. Good to know. Thanks again! Christine

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Problem BLASTING after PECAAN file transferred to DNA Master