[maker-devel] Private message regarding: MAKER run error

ohon Kin ohon.kin at gmail.com
Sun Apr 15 08:34:52 MDT 2018


grep -c ">" Ca_kacst.fna

32572

the EST i have are assembled to contigs

grep -c ">" Ca_EST

23602


grep -c ">" Ca__protein.faa

26729

these are my input-data i have reinstall perl as your instructions please
have a look, the tool still 1T not enough will stop while running of the run

i get this Error

ad$ ./maker

STATUS: Parsing control files...

WARNING: 'max_dna_len' is set too low.  The minimum value permited is
50,000.

max_dna_len will be reset to 50,000


STATUS: Processing and indexing input FASTA files...

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

HASH: Out of overflow pages.  Increase page size

Filesize limit exceeded: 25



*my maker_opt*


#-----Genome (these are always required)
genome=/Users/mohanad/Documents/maker/data/Ca_dromedarius_kacst.fna
 #genome sequence (fasta file or fasta embeded in GFF3 file)
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----Re-annotation Using MAKER Derived GFF3
maker_gff= #MAKER derived GFF3 file
est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no
altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no
model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no
pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no
other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no

#-----EST Evidence (for best results provide a file for at least one)
est=/Users/mohanad/Documents/maker/data/Ca_dromedarius_EST #set of ESTs or
assembled mRNA-seq in fasta format
altest= #EST/cDNA sequence file in fasta format from an alternate organism
est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file
altest_gff= #aligned ESTs from a closly relate species in GFF3 format

#-----Protein Homology Evidence (for best results provide a file for at
least one)
protein=/Users/mohanad/Documents/maker/data/Ca_dromedarius_V1.0_protein.faa
  #protein sequence file in fasta format (i.e. from mutiple oransisms)
protein_gff=  #aligned protein homology evidence from an external GFF3 file

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib= #provide an organism specific repeat library in fasta format for
RepeatMasker
repeat_protein= #provide a fasta file of transposable element proteins for
RepeatRunner
rm_gff= #pre-identified repeat elements from an external GFF3 file
prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change
this), 1 = yes, 0 = no
softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg
and dust filtering)

#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species= #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)
est2genome=1#infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna= #rRNA file to have Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no

#-----Other Annotation Feature Types (features MAKER doesn't recognize)
other_gff= #extra features to pass-through to final MAKER generated GFF3
file

#-----External Application Behavior Options
alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST
databases
cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI,
leave 1 when using MPI)

#-----MAKER Behavior Options
max_dna_len=10000 #length for dividing up contigs into chunks
(increases/decreases memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often
useless)

pred_flank=200 #flank for extending evidence clusters sent to gene
predictors
pred_stats=0 #report AED and QI statistics for all predictions as well as
models
AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)
min_protein=0 #require at least this many amino acids in predicted proteins
alt_splice=0 #Take extra steps to try and find alternative splicing, 1 =
yes, 0 = no
always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 =
no
map_forward=0 #map names and attributes forward from old GFF3 genes, 1 =
yes, 0 = no
keep_preds=0 #Concordance threshold to add unsupported gene prediction
(bound by 0 and 1)

split_hit=10000 #length for the splitting of hits (expected max intron size
for evidence alignments)
single_exon=0 #consider single exon EST evidence when generating
annotations, 1 = yes, 0 = no
single_length=250 #min length required for single exon ESTs if 'single_exon
is enabled'
correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes

tries=2 #number of times to try a contig if there is a failure for some
reason
clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0
= no
clean_up=0 #removes theVoid directory with individual analysis files, 1 =
yes, 0 = no
TMP= #specify a directory other than the system default temporary directory
for temporary files


On 11 April 2018 at 20:57, Carson Holt <carsonhh at gmail.com> wrote:

> The issue is with Berkley DB. BioPerl is using perl’s DB_File module to
> index the fastas.
>
> 1. Make sure you do not have an extremely large number of reads in the
> fasta files (i.e. mRNA-seq data which cannot be used directly as input to
> MAKER, you must assemble it first into transcriptome contigs)
> 2. Reinstall perl and compile against the newly installed BerkleyDB
> libraries.
> 3. Remove the brew installed BerkleyDB and use perl’s precompiled DB_File
> module.
>
> You can count reads in your fasta input using this command (replace
> file.fasta)
>
> grep -c “>” file.fasta
>
> If your counts are really high (i.e. higher than a few hundred thousand
> maximum), then you have a data issue. You are either giving too much data
> or the wrong data as input.
>
> —Carson
>
>
>
> On Apr 11, 2018, at 11:39 AM, ohon Kin <ohon.kin at gmail.com> wrote:
>
>
> hello ; Carson
>
> i really would appreciate your help im kind of having same issue
> i get this Error when i run maker i assumed that it required big memory
> space
>
> STATUS: Processing and indexing input FASTA files...
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> HASH: Out of overflow pages.  Increase page size
> Filesize limit exceeded: 25
>
> while working 1T of my Hard-disc capacity seems not enough for maker
> annotation
> i think something wrong in my input data or the dependencies
>  would you please advice on the matter and elaborate solutions please
>
> i have install BerkleyDB using brew
>
> The input giving to Maker as followed :
> Genome , EST , Protein. all in Fasta format, downloaded from NCBI --->
> then added it directly to maker for annotation
>
>  do i have to apply these data pre-process before it applied to maker
>
>
>
>
>
>
>
>
> On Thursday, 7 December 2017 19:00:52 UTC+3, Carson Holt wrote:
>>
>> The FASTA file gets indexed by BioPerl using BerkleyDB.
>>
>
>
>> I’m guessing there is something odd about your input file and the
>> database has run out of HASHes for indexing.
>>
>
>
>> You can google if there is a setting you can configure in BerkleyDB on
>> Mac.
>>
>
>
>> But I suspect you are doing something like giving the raw reads from an
>> mRNA-seq experiment or DNA sequencing to MAKER (resulting in billions of
>> entrires to be indexed), which would be incorrect. MAKER can’t handle raw
>> data. You must first assemble it using using like Trinity for example for
>> mRNA.
>>
>> Thanks,
>> Carson
>>
>> On Dec 7, 2017, at 8:53 AM, Scott Cain <sc... at scottcain.net> wrote:
>>
>> Hi Guinara,
>>
>> I don't know (though my guess would be that you're running out of
>> memory).  I'm cc'ing the MAKER developer's mailing list to see if anybody
>> on that list knows.
>>
>> Scott
>>
>>
>> On Wed, Dec 6, 2017 at 8:36 PM, Gulnara Tagirdzhanova <tagi... at ualbert
>> a.ca> wrote:
>>
>>> Hello,
>>>
>>> I got this error running maker on mac:
>>>
>>> STATUS: Parsing control files...
>>> STATUS: Processing and indexing input FASTA files...
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> HASH: Out of overflow pages. Increase page size
>>> Filesize limit exceeded: 25
>>>
>>> Is there anything that could solve it?
>>>
>>> Thank you,
>>> Gulnara
>>>
>>>
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> maker-devel mailing list
>> maker... at box290.bluehost. <http://box290.bluehost.com/>com
>> <http://box290.bluehost.com/>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>


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