[maker-devel] Maker ERROR

[José Mª G. Perez-Silva]

Hi,

I wrote early this day, in reference to a problem of (apparently) space.
After I deleted some unnecesary files (despite having plenty of storage
left), I killed all the processes, and set 'clean_try=1' as recomended in
this post
<http://gmod.827538.n3.nabble.com/Re-re-run-MAKER-after-out-of-disk-space-td3708059.html>.
Before re-running the processes, we checked that there were no limitation
over the size of a directory or something similar.

After re-running, at first, all seemed correct, but when I re-checked some
time after, I found out a lot of contigs with the status FAILED without
folder specification in the '_master_datastore_index.log', looking like:

Contig480 FAILED
>
Contig496 FAILED

Contig512 FAILED

Contig528 FAILED

Contig544 FAILED

Contig560 FAILED​


But checking the 'nohub.out' of every proccess (16 in total, as the machine
has 16 cores), I notice that each run is, from time to time, processing the
contig correctly. So, after several (a lot) of FAILED contigs, it process
one correctly. As said in the previous email, the ERROR dispolayed in the
nohup.out is (including the last part of a processed contig at the
beguinning):

​
> #--------- command -------------#

Widget::blastx:

/usr/bin/blastall -p blastx -d
> /data/ge/tmp/maker_VfDQQU/hsap_ensembl%2Efa.mpi.10.6 -i
> /data/ge/tmp/maker_VfDQQU/0/Contig20.0 -b 10000 -v 10000 -e 1e-06 -z 300 -Y
> 500000000 -a 4 -U -F T -I T -o
> /data/ge/round3/cg.maker.output/cg_datastore/56/AC/Contig20//theVoid.Contig20/0/Contig20.0.hsap_ensembl%2Efa.blastx.temp_dir/hsap_ensembl%2Efa.mpi.10.6.blastx

#-------------------------------#

deleted:511 hits

doing blastx of proteins

open3: fork failed: Cannot allocate memory at
> /home/jmgps/software/maker/bin/../lib/File/NFSLock.pm line 1037.

--> rank=NA, hostname=Planarian2

ERROR: Failed while doing blastx of proteins

ERROR: Chunk failed at level:8, tier_type:3

FAILED CONTIG:Contig20


> ERROR: Chunk failed at level:4, tier_type:0

FAILED CONTIG:Contig20


> examining contents of the fasta file and run log

ERROR: could not make datastore directory

--> rank=NA, hostname=Planarian2

ERROR: Failed while examining contents of the fasta file and run log

ERROR: Chunk failed at level:0, tier_type:0

FAILED CONTIG:Contig22


> examining contents of the fasta file and run log

ERROR: could not make datastore directory

--> rank=NA, hostname=Planarian2

ERROR: Failed while examining contents of the fasta file and run log

ERROR: Chunk failed at level:0, tier_type:0

FAILED CONTIG:Contig24


> examining contents of the fasta file and run log

ERROR: could not make datastore directory

--> rank=NA, hostname=Planarian2

ERROR: Failed while examining contents of the fasta file and run log

ERROR: Chunk failed at level:0, tier_type:0

FAILED CONTIG:Contig26


> examining contents of the fasta file and run log

ERROR: could not make datastore directory

--> rank=NA, hostname=Planarian2

ERROR: Failed while examining contents of the fasta file and run log

ERROR: Chunk failed at level:0, tier_type:0

FAILED CONTIG:Contig28​


I'm totally lost here, I think it is still processing contigs, but the
FAILED attemps slow down the whole process, and we are in a hurry due to
the maintenance of the machine. And I can't understand the source of the
ERROR.

I will be more than happy to provide more details about the problem, if
requested.

Thanks a lot for the help!
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