Hi,
I don't manage to send my file for annotation on mercator. It worked before, but now the server send me this message:
Error: Error creating job directory '/data/mercator/work/Mercator242f360caac71b6d5297fa7d750b1537'

How can I solve my problem?
Thanks
Emilie

We currently have a very slow file system which causes time outs, we hope to have that fixed in 24h.

Axel

Dear Emilie,

our problems seem to be fixed.
My recent run of mercator ran fine.
So you are welcome to test.

sorry for the inconvinience
Axel

Hi,
I made a test this morning, and it works!
Thanks
emilie

My question: I am working on Mercator. I have ~4 fasta files, 30,000 seqs and ~12x10^6 nucleotides/file (<maximum of Mercator is 30 x10^6 nucleotides). My sequences are ESTs of plant tissues that were generated by Pacbio sequencing with 15% error rate. I already had 2 successful jobs with 2 files - but only ~2% assigned. However, recently two jobs (from the same files) were failed. Should I request a job for a larger data set?

Answer from Marc (via email, published here with his agreement): We are currently working on the mercator pipeline and web interface. Unfortunately that can cause temporary instabilities and be apologize for that. Especially larger, long-running jobs are prone to be affected and hence i'd suggest that you sent the data via email (or dropbox if they're too big) and i submit them manually.

My solution: I will split my big fasta files into smaller ones (biopython) to see if this works. If not, I will send Marc my files.

ah no please send us the file. The whole idea behind the limitation is to not infere with large jobs. Also if we have such a low assigment rate, we could trouble shoot the assignemts with your permission, if you wanted.

Best Wishes,
Björn

Hello,

I sent the large file to Marc on May 22. However, I have not heard back. Could you please let me know if the file helped?

I also have another question regarding new database usage appearance. Recently, I have been using Mercator to run Fasta file < 10 x 10^6 nucleotides.
This is one of my requests:
MULTIPLE: 1
TAIR: 1
PPAP: 1
ORYZA: 1
CHLAMY: 1
IPR: 1
BLAST_CUTOFF: 80
KOG: 1
ANNOTATE: 1
CDD: 1
CONSERVATIVE: 1
Sequences: 5000
Nucleotides: 5629835

This is the running process when it finishes:
JobStatus: METAMONSTER

IPR Aug 13, 2012 6:35:14 PM
0% 100%
PPAP Aug 13, 2012 6:35:14 PM
0% 0%
TAIR Aug 13, 2012 6:35:14 PM
0% 0%
KOG Aug 13, 2012 6:35:14 PM
0% 100%
CDD Aug 13, 2012 6:35:14 PM
0% 100%
CHLAMY Aug 13, 2012 6:35:14 PM
0% 0%
ORYZA Aug 13, 2012 6:35:14 PM
0% 0%

I am wondering if the other databases (e.g.: PPAP, ORYZA) were utilized?

Thank you,

Hi Happyfly,

your mapping job is running and will soon be finished. I am sorry
for the delay .

cheers,
Marc

Dear Mercator developpers,

I have the same problem.

I would like to make a bin mapping file for apple (malus x domestica)
out of my 5771 genes of interest, ca.73% received no bin annotation and with Blast2Go I got them.
I wrote you an e-mail but no answer so far.
I hope you could help me to resolve this problem.
all the bests
Michele

Dear Michele,

i quickly checked your job to find out where the problem lies and found out that you had
submitted nucleotide data but configured the job to work with protein data. Please resubmit
your data and configure mercator to run with nucleotide data by clicking the "IS_DNA"
checkbox.

Best greetings,
Marc

Thank you very much! My sequences were checked in all of the libraries in Mapman.