[maker-devel] MAKER run error -with blast

Tue Aug 26 08:53:25 MDT 2014

Hi,

I have been using MAKER for a while and its been running fine. Recently I am encountering an error (attaching the error from the error log file - error1.txt).

As input I am providing the fasta file of a scaffold, a transcriptome dataset(in gff) and a protein dataset (as fasta). These kind of input files have run successfully in the past.

The file that is reported as 'No such file or directory at' in the error ouptut changes in different runs.

To make sure I wasn't doing something wrong, I reran a dataset that had run successfully before, but I get an error with that too. (error log attached as error2.txt).

The only difference in this run, previously I ran it for the entire genome, and now I am testing it on just one scaffold.

Would you have any idea of why this might be happening?

Thanks,

Ranjani

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total clusters:6 now processing 0
prepare section files
Gathering GFF3 input into hits - chunk:18
prepare section files
Gathering GFF3 input into hits - chunk:19
Removing file: /lustre1/escratch1/ranjani_Jul_23/sn1_comparisons/maker_with_sn1prot/correct_uniprot_sn1prot_gff/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.7.end.section.holdover
ERROR: No such file or directory at /lustre1/escratch1/ranjani_Jul_23/sn1_comparisons/maker_with_sn1prot/correct_uniprot_sn1prot_gff/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.7.end.section.holdover
 at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Process/MpiChunk.pm line 4482.
	Process::MpiChunk::__ANON__() called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Error.pm line 408
	eval {...} called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Error.pm line 407
	Error::subs::try(CODE(0x12f4d0f8), HASH(0x129acca0)) called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Process/MpiChunk.pm line 4491
	Process::MpiChunk::retrieve("/lustre1/escratch1/ranjani_Jul_23/sn1_comparisons/maker_with_"...) called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Process/MpiChunk.pm line 3311
	Process::MpiChunk::__ANON__() called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Error.pm line 415
	eval {...} called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Error.pm line 407
	Error::subs::try(CODE(0x1262ed50), HASH(0x12409548)) called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Process/MpiChunk.pm line 4215
	Process::MpiChunk::_go(Process::MpiChunk=HASH(0x12eb0f70), "run", HASH(0x12958360), 12, 3) called at /panfs/pstor.storage/rcclocal/zcluster/maker/2.31.5-mpich2/bin/../lib/Process/MpiChunk.pm line 341
	Process::MpiChunk::run(Process::MpiChunk=HASH(0x12eb0f70), 5) called at /usr/local/maker/latest/bin/maker line 979
--> rank=5, hostname=compute-6-5.local
--> rank=5, hostname=compute-6-5.local
ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:scaffold00001
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STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore

To access files for individual sequences use the datastore index:
/panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log

--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold00001
Length: 11360811
#---------------------------------------------------------------------

setting up GFF3 output and fasta chunks
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_8GDzH7; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.0.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_1sNfMC; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.6.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_isHjoB; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.1.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_isHjoB; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.2.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_isHjoB; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.5.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_isHjoB; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.3.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /lscratch/tmp/5603554.1.rcc-30d/maker_isHjoB; /panfs/pstor.storage/rcclocal/zcluster/repeatmasker/4.0.1/RepeatMasker /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0/scaffold00001.4.Alveolata.rb -species Alveolata -dir /panfs/pstor.storage/grphomes/jcklab/i_000059/Mero_strand_specific_04142014/maker_final_ssCuff_uniprotTop/retry_scf1/scaffold00001.maker.output/scaffold00001_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/0 -pa 1
#-------------------------------#
WUBlastSearchEngine::search: FATAL:  There is nothing in the requested database to search!

WARNING: Comparison failed. Retrying with larger minmatch (10)
WUBlastSearchEngine::search: FATAL:  There is nothing in the requested database to search!