OMA cannot evaluate boolean
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2.9 years ago
thomasbersez ▴ 50

Hi!

I am trying to run OMA standalone on a two proteome test set. All parameters are left to default. I get the following error :

OMA -c

Starting database conversion and checks...
Process 19349 on pac-1052-998: job nr 1 of 1
Error, (in ConvertGenomes) cannot evaluate boolean

Any idea on how to fix it?

OMA orthologs bug issue • 846 views
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2.9 years ago

Hi Thomas

the error indicate that some parameter is undefined or alternatively the input data might be not in the right format. Could you please rerun OMA Standalone with higher verbosity level, i.e. by running it as OMA -c -d 3 which should produce a more informative error message in general.

Adrian

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2.9 years ago
thomasbersez ▴ 50

Hi,

Thanks for your quick answer! I get the following message with OMA -c -d 3.

only_run_dbconv := true
# SetRandSeed: SetRand(399990844):
Starting database conversion and checks...
Process 9707 on pac-1052-998: job nr 1 of 1
Error, (in ConvertGenomes) cannot evaluate boolean
        executing statement: if pinf[ProcNr] = 1 and not ReuseCachedResults then
'...' fi
        locals defined as: dataset_hash = 4b443254a3ebf7a9ecd53b56072e3e0889087\
aed77a86ac615ee67007197d6501ad605fa6d97dcd8216cff30538478323a76114f911a6a5ac108\
4bd7dba3e493, g = g, off = off, gname = gname, checksum = checksum, spliceFn = 
spliceFn, fcheck = fcheck, code = code, input = input, ML = ML, splicemap = 
splicemap, setNr = setNr, step = step, start = start, end_pos = end_pos, i = i
        ConvertGenomes called with arguments: [DB/ecoli_protein.fa, 
DB/thetaiotaomicron_protein.fa], ParallelInfo(1,1)

Thanks again for helping!

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2.9 years ago
thomasbersez ▴ 50

Edit,

I have managed to solve the previous error. It was just an error in the parameters.drw file ... Sorry for the bothering ^^

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no worries. good to hear!

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2.9 years ago
thomasbersez ▴ 50

Just an other point,

Now I get this error,

1) Mem: 0.017GB (UINT)s=76983683, lostorage=76234752, cond=0
(UINT)s=76983683, historage=157437752, cond=0 strlen(s)=0, s=,
s=76983683 strlen(s2)=0, s2=, s2=76983684 Irrecoverable system error
 gc-14 running Align Aborted (core dumped)

when running the full pipeline.

This seems to be cause by a RAM usage overflow. I ran a memory usage sampling using the sample-memory-usage command. The needed allocation goes beyond my poor 8Gb of RAM. I won't do my test locally!

Best, Thomas

.

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