[maker-devel] (no subject)

[Scott Cain]

Hi Sangramjit,

I'm cc'ing the MAKER mailing list, where they should be able to help you
out.

Scott


On Tue, Apr 7, 2015 at 3:57 AM, sangramjit basu <officialsjb at gmail.com>
wrote:

>
>
> *Hello Sir/Madam,*
>
> *I am Bioinformatician trainee on NGS platform. I have been trying to use
> Maker to annotate rice genome (Oryza sativa indica), but have been facing a
> error that i cannot understand:*
> setting up GFF3 output and fasta chunks
> doing repeat masking
> ERROR: Not a SCALAR reference
>  at /opt/maker/bin/../lib/Fasta.pm line 382.
>     Fasta::_formatSeq(FastaSeq=HASH(0x4219e18), 60) called at
> /opt/maker/bin/../lib/Fasta.pm line 369
>     Fasta::toFastaRef(">1 CHUNK number:0 size:100000 offset:0",
> REF(0x4207be0)) called at /opt/maker/bin/../lib/FastaChunk.pm line 217
>     FastaChunk::fasta_ref(FastaChunk=HASH(0x417e968)) called at
> /opt/maker/bin/../lib/FastaChunk.pm line 168
>     FastaChunk::write_file(FastaChunk=HASH(0x417e968),
> "/opt/maker/Oryza_indica.ASM465v1.25.dna.chromosome.1.maker.ou"...) called
> at /opt/maker/bin/../lib/GI.pm line 3138
>     GI::repeatmask(FastaChunk=HASH(0x417e968),
> "/opt/maker/Oryza_indica.ASM465v1.25.dna.chromosome.1.maker.ou"..., 1,
> "simple", "/opt/RepeatMasker/RepeatMasker", "", 1, runlog=HASH(0x4207cb8))
> called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 769
>     Process::MpiChunk::__ANON__() called at /opt/maker/bin/../lib/Error.pm
> line 415
>     eval {...} called at /opt/maker/bin/../lib/Error.pm line 407
>     Error::subs::try(CODE(0x417fce0), HASH(0x4195a48)) called at
> /opt/maker/bin/../lib/Process/MpiChunk.pm line 4224
>     Process::MpiChunk::_go(Process::MpiChunk=HASH(0x417fc80), "run",
> HASH(0x4208f70), 0, 1) called at /opt/maker/bin/../lib/Process/MpiChunk.pm
> line 341
>     Process::MpiChunk::run(Process::MpiChunk=HASH(0x417fc80), 0) called at
> /opt/maker/bin/../lib/Process/MpiChunk.pm line 357
>     Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x417fc80), 0)
> called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287
>     Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x417fc20), 0)
> called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287
>     Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x4102ba8), 0)
> called at /opt/maker/bin/maker line 686
> --> rank=NA, hostname=nucleome01-Lenovo-H520S
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:1
>
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:1
>
> *P.S. : I have low hard disk space, is it because of that ??*
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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