[maker-devel] Support on maker

[Marvin B Moore]

Hi Gez,

I’m forwarding you e-mail to the maker-devel mailing list for support.  This mailing list is a good place to direct questions like this one.  If you aren’t aleady a member of this mailing list, I’d highly recommend you join here:

http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

Cheers,

Barry

From: Gezahegn Girma <ggirmate at purdue.edu>
Date: Thursday, October 28, 2021 at 12:19 PM
To: Marvin B Moore <barry.moore at genetics.utah.edu>
Subject: Support on maker
Hi Barry,

I am using maker for genome annotation of sorghum genotype.

Maker is running and keep increasing the log file but I see the following error messages. Kindly, this is to request for your kind support to resolve this issue.

=========================================================
STATUS: Now running MAKER...
WARNING: Cannot find >0, trying to re-index the fasta.
stop here: 0
ERROR: Fasta index error
 at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239.
        Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31.
10-nompi/bin/../lib/Process/MpiTiers.pm line 73
          Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415
         eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407
          Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT
iers.pm line 79
        Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/
Process/MpiTiers.pm line 56
         Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3
1.10-nompi/bin/maker line 669
--> rank=NA, hostname=bell-a105.rcac.purdue.edu<http://bell-a105.rcac.purdue.edu>
ERROR: Failed in tier preparation
examining contents of the fasta file and run log
.
.
.
Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its
translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
================================================================================
Regards,
Gez


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