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Re: [ModPipe-users] MODELLER bug report
- To: Help and discussion for users of ModPipe <modpipe-users AT salilab.org>
- Subject: Re: [ModPipe-users] MODELLER bug report
- From: Marco Galardini <marco AT ebi.ac.uk>
- Date: Fri, 06 Jun 2014 13:29:25 +0100
- Reply-to: Help and discussion for users of ModPipe <modpipe-users AT salilab.org>
Hi Ben,
thanks for your prompt reply: the problem is that the PSSM file should
be ok.
the conf file has these values:
XPRF_LIST /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.list
XPRF_PSSMDB /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.pssm
the files in that location are there and not empty:
$ ls -lh
total 1.3G
-rw-r--r-- 1 [...] [...] 3.7M Jun 5 09:53 pdb95_prf.list
-rw-r--r-- 1 [...] [...] 1.1G Jun 5 09:55 pdb95_prf.pssm
$ head -n 1 pdb95_prf.list
/nfs/[...]/modpipe-2.2.0/dbs/pdb95/data/2a/12asA/12asA-uniprot90.prf
$ head pdb95_prf.pssm
/nfs/[...]/modpipe-2.2.0/dbs/pdb95/data/2a/12asA/12asA-uniprot90.prf
327
583 405 409 421 336 436 371 355 421 355 386
450 386 421 386 646 471 379 286 336
336 336 286 318 690 286 492 409 318 409 409
318 268 353 318 336 336 386 518 764
357 347 256 280 392 216 261 700 412 520 507
267 266 289 292 311 357 567 260 349
468 258 588 583 268 280 622 310 348 496 335
356 287 588 396 509 394 339 224 306
363 298 346 416 286 286 340 334 550 458 383
381 329 668 495 430 646 354 281 314
374 274 434 566 282 321 420 294 470 365 421
420 371 760 466 421 374 332 319 369
377 221 403 602 226 303 322 379 573 343 327
337 288 721 516 342 452 408 223 274
663 318 353 580 255 372 455 285 458 294 322
331 320 602 443 400 404 334 235 291
Any other parameter or file I should look for?
Many thanks,
Marco
On 05/06/2014 19:55, Ben Webb wrote:
On 6/5/14, 6:03 AM, Marco Galardini wrote:
*alloc_p_215E> Dynamic memory allocation failed.**
** Routine, variable, status: ipssm 3**
This happens if you give Modeller an empty PSSM database (it tries to
allocate 0 bytes of memory to store it). It's already "fixed" in the
upcoming 9.14 release, in that it'll give you a more intelligible
error message, but the underlying cause is that something is wrong
with your PSSM file.
Ben