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Old 08-27-2014, 08:01 PM   #1
bioman1
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Location: US

Join Date: May 2012
Posts: 80
Unhappy Trouble running CEGMA sample data

Hello,

I am installing cegma for the first time and I am having trouble running sample data. I googled it, I could not able to find a solution. I followed steps exactly as described in http://korflab.ucdavis.edu/Datasets/...ructions_2.txt

Any suggestions will be greatly appreciated!



user:~/cegma_v2.4.010312/bin$ ./cegma -g /home/src/cegma_v2.4.010312/sample/sample.dna -p /home/src/cegma_v2.4.010312/sample/sample.prot


********************************************************************************
** MAPPING PROTEINS TO GENOME (TBLASTN) **
********************************************************************************

RUNNING: genome_map -n genome -p 6 -o 5000 -c 2000 -t 1 /home/src/cegma_v2.4.010312/sample/sample.prot /home/src/cegma_v2.4.010312/sample/sample.dna 2>output.cegma.errors


Building a new DB, current time: 08/28/2014 11:41:29
New DB name: /tmp/genome12011.blastdb
New DB title: /home/src/cegma_v2.4.010312/sample/sample.dna
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1 sequences in 0.167003 seconds.
Found 86 candidate regions in /home/src/cegma_v2.4.010312/sample/sample.dna


********************************************************************************
** MAKING INITIAL GENE PREDICTIONS FOR CORE GENES (GENEWISE + GENEID) **
********************************************************************************

RUNNING: local_map -n local -f -h ./data/hmm_profiles -i KOG genome.chunks.fa 2>output.cegma.errors
FATAL ERROR when running local map 6400: "No such file or directory"

---------------------------------------------------------

less output.cegma.errors

Warning Error
Could not open ./data/hmm_profiles/KOG0292.hmm for HMM reading
Warning Error
Could not read hmm from ./data/hmm_profiles/KOG0292.hmm

Fatal Error
Could not build objects!
Can't run genewise -splice_gtag -quiet -gff -pretty -alb -hmmer ./data/hmm_profiles/KOG0292.hmm /tmp/genomic13567.fa > /tmp/genewise13567
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Old 08-28-2014, 02:59 AM   #2
GenoMax
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Location: East Coast USA

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You may have followed the steps in the link you included but did you get any errors along the way?

Is there a local "bin" directory in the cegma base directory and are there several files in there including "local_map"?
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Old 08-31-2014, 06:50 PM   #3
peromhc
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Location: Durham, NH

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I made an amazon machine image for CEGMA - search CEGMA on AWS and you should find it. It is ami-18935a70. It's preconfigured, just upload your data and run.
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Old 09-08-2014, 07:45 AM   #4
kbradnam
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From the location where you ran CEGMA, is there a valid path to ./data/hmm_profiles?
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