Question: OMA cannot evaluate boolean
0
gravatar for thomasbersez
4 months ago by
thomasbersez20
France INRA
thomasbersez20 wrote:

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?

bug issue oma orthologs • 211 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by thomasbersez20
0
gravatar for adrian.altenhoff
4 months ago by
Switzerland
adrian.altenhoff620 wrote:

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

ADD COMMENTlink written 4 months ago by adrian.altenhoff620
0
gravatar for thomasbersez
4 months ago by
thomasbersez20
France INRA
thomasbersez20 wrote:

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!

ADD COMMENTlink written 4 months ago by thomasbersez20
0
gravatar for thomasbersez
4 months ago by
thomasbersez20
France INRA
thomasbersez20 wrote:

Edit,

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

ADD COMMENTlink written 4 months ago by thomasbersez20

no worries. good to hear!

ADD REPLYlink written 4 months ago by adrian.altenhoff620
0
gravatar for thomasbersez
4 months ago by
thomasbersez20
France INRA
thomasbersez20 wrote:

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

.

ADD COMMENTlink written 4 months ago by thomasbersez20
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