From samuel.decker at student.montana.edu  Tue Jan 31 12:28:09 2023
From: samuel.decker at student.montana.edu (Decker, Samuel)
Date: Tue, 31 Jan 2023 19:28:09 +0000
Subject: [maker-devel] Maker error after calling SNAP
Message-ID: <BL3PR02MB8001FABB56A97D403269C762A2D09@BL3PR02MB8001.namprd02.prod.outlook.com>

Hi,
I am trying to run maker on Camelina Sativa, and it runs smoothly for the most part until it reaches a certain stage in SNAP.  Maker passes a short sequence to SNAP to predict genes on, but that sequence is more than half N's, and SNAP fails, leading to maker calling that chunk as a failure and ending the run.

When looking at the Widget call, it seems that for some reason the .hmm file is not included in the command sent to SNAP.  I manually ran the command with the .hmm file included and it seems to execute, though no output file is produced.

After speaking with Ian Korf, he seemed to think it was an error relating to the very short and ambiguous (many N's) fasta file that maker passed to SNAP.

So two questions: Why did the .hmm file not get passed to SNAP as part of the command, and why did maker send such a short chunk to SNAP for gene prediction?

I've attached a text file with the command and the error log, the fasta that maker is sending to SNAP, and the xdef file as well.

Thank you for your help,
Samuel Decker
PhD Student
Montana State University
Plant Sciences/Plant Pathology
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#--------- command -------------#
Widget::snap:
/usr/bin/snap -plus -xdef /home/nostril/maker_stuff/results.maker.output/results_datastore/07/64/CHR_4//theVoid.CHR_4/172_0.18616337-18617933.CS.hmm.auto_annotator.xdef.snap  /home/nostril/maker_stuff/results.maker.output/results_datastore/07/64/CHR_4//theVoid.CHR_4/172_0.18616337-18617933.CS.hmm.auto_annotator.snap.fasta > /home/nostril/maker_stuff/results.maker.output/results_datastore/07/64/CHR_4//theVoid.CHR_4/172_0.18616337-18617933.CS.hmm.auto_annotator.snap
#-------------------------------#

SNAP - Semi-HMM-based Nucleic Acid Parser (version 2006-07-28)

usage: snap [options] <HMM file> <FASTA file> [options]
options:
  -help           report useful information
  -lcmask         treat lowercase as N
  -plus           predict on plus strand only
  -minus          predict on minus strand only
  -gff            output annotation as GFF
  -ace            output annotation as ACED
  -quiet          do not send progress to STDERR
  -aa <file>      create FASTA file of proteins
  -tx <file>      create FASTA file of transcripts
  -xdef <file>    external definitions
  -name <string>  name for the gene [default snap]
ERROR: Snap failed
--> rank=NA, hostname=DESKTOP-AD6C0QF
--> rank=NA, hostname=DESKTOP-AD6C0QF
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:CHR_4

deleted:0 genes
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:CHR_4

>CHR_4 172_0 offset:18616337
AATCTGTGATTTGCAGAAAACCCTTAAAAATATTTGTAATTTGCATAATCCTTATAAAAT
CCTACCAATTGATGTTTAATGGTTTTTTCCCCACCCACAAACCCAACACAAACCCAATCG
GATCTCTCTCGGATCTATTTACCCCCACTATTTCTTTTAATTTCAAACAATGGTTTTCTC
TCTCTCTTCTTGAAAAACTAGGGATTACTAATCGAGAGATCATTTGCTCTCTTTGATTGT
TGTGTTGTTCGATCGATTGTGGAGACTCATCGATTGTTAGCAGTTagatgaatatgagga
agaacaataagaagagaaaaattgccgaggaagaacaagaTTCGGAACCGGGGGAGAGTT
CACAGCCGGCGGATCTCCCTGCGGCTGGTGATGGAGATGGTGAGGATGAAGTCGAAAGGA
GTGATAAAGAGGATGAGGGAGTCGACTCAGAGACTTCGGGAGATGATGAGAAGGGAGACG
AGGAGGATGTCGGAAGTGACGAAGGAGAAGAAGAGAGCGAGCCAGATCTCGTTGGCGAAG
GAGAAGTAGATTTGGACGCATCCTTGGGAGAGACAGATTCGGGCGACTCCACCGAGGCAA
TGGTACGTAGTACCGATTGATTGACCATGTAGAAGTAGGGAAAACATATTTTTTTCTGGG
TTTGTAATACTAGGATAACATAGTATAACTGTTTNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

>xdef file offset: 18616337 i_flank:2
Coding  294     602     +       0.2     .       .       .       ADJ
Coding  803     836     +       0.2     .       .       .       ADJ
Intron  604     801     +       1000    .       .       .       ADJ
Coding  604     801     +       -100    .       .       .       ADJ

From samuel.decker at student.montana.edu  Tue Jan 31 12:28:09 2023
From: samuel.decker at student.montana.edu (Decker, Samuel)
Date: Tue, 31 Jan 2023 19:28:09 +0000
Subject: [maker-devel] Maker error after calling SNAP
Message-ID: <BL3PR02MB8001FABB56A97D403269C762A2D09@BL3PR02MB8001.namprd02.prod.outlook.com>

Hi,
I am trying to run maker on Camelina Sativa, and it runs smoothly for the most part until it reaches a certain stage in SNAP.  Maker passes a short sequence to SNAP to predict genes on, but that sequence is more than half N's, and SNAP fails, leading to maker calling that chunk as a failure and ending the run.

When looking at the Widget call, it seems that for some reason the .hmm file is not included in the command sent to SNAP.  I manually ran the command with the .hmm file included and it seems to execute, though no output file is produced.

After speaking with Ian Korf, he seemed to think it was an error relating to the very short and ambiguous (many N's) fasta file that maker passed to SNAP.

So two questions: Why did the .hmm file not get passed to SNAP as part of the command, and why did maker send such a short chunk to SNAP for gene prediction?

I've attached a text file with the command and the error log, the fasta that maker is sending to SNAP, and the xdef file as well.

Thank you for your help,
Samuel Decker
PhD Student
Montana State University
Plant Sciences/Plant Pathology
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#--------- command -------------#
Widget::snap:
/usr/bin/snap -plus -xdef /home/nostril/maker_stuff/results.maker.output/results_datastore/07/64/CHR_4//theVoid.CHR_4/172_0.18616337-18617933.CS.hmm.auto_annotator.xdef.snap  /home/nostril/maker_stuff/results.maker.output/results_datastore/07/64/CHR_4//theVoid.CHR_4/172_0.18616337-18617933.CS.hmm.auto_annotator.snap.fasta > /home/nostril/maker_stuff/results.maker.output/results_datastore/07/64/CHR_4//theVoid.CHR_4/172_0.18616337-18617933.CS.hmm.auto_annotator.snap
#-------------------------------#

SNAP - Semi-HMM-based Nucleic Acid Parser (version 2006-07-28)

usage: snap [options] <HMM file> <FASTA file> [options]
options:
  -help           report useful information
  -lcmask         treat lowercase as N
  -plus           predict on plus strand only
  -minus          predict on minus strand only
  -gff            output annotation as GFF
  -ace            output annotation as ACED
  -quiet          do not send progress to STDERR
  -aa <file>      create FASTA file of proteins
  -tx <file>      create FASTA file of transcripts
  -xdef <file>    external definitions
  -name <string>  name for the gene [default snap]
ERROR: Snap failed
--> rank=NA, hostname=DESKTOP-AD6C0QF
--> rank=NA, hostname=DESKTOP-AD6C0QF
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:CHR_4

deleted:0 genes
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:CHR_4

>CHR_4 172_0 offset:18616337
AATCTGTGATTTGCAGAAAACCCTTAAAAATATTTGTAATTTGCATAATCCTTATAAAAT
CCTACCAATTGATGTTTAATGGTTTTTTCCCCACCCACAAACCCAACACAAACCCAATCG
GATCTCTCTCGGATCTATTTACCCCCACTATTTCTTTTAATTTCAAACAATGGTTTTCTC
TCTCTCTTCTTGAAAAACTAGGGATTACTAATCGAGAGATCATTTGCTCTCTTTGATTGT
TGTGTTGTTCGATCGATTGTGGAGACTCATCGATTGTTAGCAGTTagatgaatatgagga
agaacaataagaagagaaaaattgccgaggaagaacaagaTTCGGAACCGGGGGAGAGTT
CACAGCCGGCGGATCTCCCTGCGGCTGGTGATGGAGATGGTGAGGATGAAGTCGAAAGGA
GTGATAAAGAGGATGAGGGAGTCGACTCAGAGACTTCGGGAGATGATGAGAAGGGAGACG
AGGAGGATGTCGGAAGTGACGAAGGAGAAGAAGAGAGCGAGCCAGATCTCGTTGGCGAAG
GAGAAGTAGATTTGGACGCATCCTTGGGAGAGACAGATTCGGGCGACTCCACCGAGGCAA
TGGTACGTAGTACCGATTGATTGACCATGTAGAAGTAGGGAAAACATATTTTTTTCTGGG
TTTGTAATACTAGGATAACATAGTATAACTGTTTNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

>xdef file offset: 18616337 i_flank:2
Coding  294     602     +       0.2     .       .       .       ADJ
Coding  803     836     +       0.2     .       .       .       ADJ
Intron  604     801     +       1000    .       .       .       ADJ
Coding  604     801     +       -100    .       .       .       ADJ