[Transdecoder-users] error with cdna_alignment_orf_to_genome_orf.pl

[Will J. <wil...@gm...>]

Hi guys,
I am trying to run cdna_alignment_orf_to_genome_orf.pl but am getting this
error:

Use of uninitialized value $info in pattern match (m//) at
/home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/
cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1.
Use of uninitialized value $info in concatenation (.) or string at
/home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/
cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1.
Error, cannot parse ID from  at
/home/will/devel/bioinfo/trinity/trinity-plugins/transdecoder/
cdna_alignment_orf_to_genome_orf.pl line 108, <$fh> line 1.

As inputs I am using are:
GFF3 file produced by transdecoder of transcripts produced by the PASA
annotation comparison and update process.
I used bedtools getfasta -name to get the fasta sequences for the
transcripts produced by PASA. I then ran them through transdecoder to get
the cds and gff3 files, then I used the seqclean utility from trinity to
remove some (195) low quality ORFs.

The 'transcripts.gff3' file (2nd positional argument) I am using is the one
produced by PASA annotation comparison and update.

Below is the head of each file:
$ head GG_MAKER_UPDATE_ORFs.transdecoder.gff3
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       gene    315     1454    .       -       .
ID=g.59;Name=ORF%20g.59%20m.59%20type%3Acomplete%20len%3A380%20%28-%29
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       mRNA    315     1454    .       -       .       ID=m.59;Parent=g.59
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       exon    315     1454    .       -       .
ID=m.59.exon1;Parent=m.59
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       CDS     315     1454    .       -       .
ID=cds.m.59;Parent=m.59

ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       gene    1570    2298    .       -       .
ID=g.60;Name=ORF%20g.60%20m.60%20type%3Acomplete%20len%3A243%20%28-%29
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       mRNA    1570    2298    .       -       .       ID=m.60;Parent=g.60
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       exon    1570    2298    .       -       .
ID=m.60.exon1;Parent=m.60
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18
.       CDS     1570    2298    .       -       .
ID=cds.m.60;Parent=m.60

head APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3
==> APLG003vsItGsH_mydb_pasa.gene_structures_post_PASA_updates.61104.gff3
<==
# ORIGINAL: genemark-scaffold_1446-processed-gene-0.1-mRNA-1 original gene
structure, not modified by PASA
scaffold_1446   maker   gene    6232    6658    .       -       .
ID=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1
scaffold_1446   maker   mRNA    6232    6658    .       -       .
ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1;Name=genemark-scaffold_1446-processed-gene-0.1
scaffold_1446   maker   exon    6617    6658    .       -       .
ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1
scaffold_1446   maker   CDS     6617    6658    .       -       0
ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1
scaffold_1446   maker   exon    6232    6534    .       -       .
ID=genemark-scaffold_1446-processed-gene-0.1-mRNA-1.exon2;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1
scaffold_1446   maker   CDS     6232    6534    .       -       0
ID=cds.genemark-scaffold_1446-processed-gene-0.1-mRNA-1;Parent=genemark-scaffold_1446-processed-gene-0.1-mRNA-1


#PROT genemark-scaffold_1446-processed-gene-0.1-mRNA-1
genemark-scaffold_1446-processed-gene-0.1
 MDAEDTRSALIWWKERQGKYPILSSLARDYLACSASSCAAERTFSAAADVCPGNRGKLLPRTIEMCVSSRMWLKDKVPVTGDFEAANNIVQKFTAFKEKNRLNTIDPSPDITKK*

>m.60 g.60  ORF g.60 m.60 type:complete len:243 (-)
ID=augustus_masked-scaffold_0-processed-gene-1.18-mRNA-1;augustus_masked-scaffold_0-processed-gene-1.18:1570-2298(-)
ATGACCAAACCGTGCGTTCATAATCCCCTCAATTCGTCTCGCCTTGATTCTACGCCTCAG
TTGACAGGATTATACGTGTTGTCACCGAACTTCATCATCTCTAAATATAAGATTACTCAA
TATGACCTTTCGAACGTGTCCACCATACAAAATGCCGCATCAGATTCATTATCCGTCGAT
CCTTCACATCGCCCCATGCCTGGCACAAGATCTCGTGGAGGAGGCGGGGATATGTCATTG
GATCCTCCCATCTCGACTAGCAATGAGAAACCGGTATTGACAAAAAAGTCGAGCATCATT
TTCCCAGTCCCTGTAAATCACTGTAGCATCAGTCCAGACTCAAAATCGATGGTGGCCGTA
GGCGATAGTAGCGAAGTGTTTATATATGACTGTCAAAATGCACATCAATCAAATGAACCG
TTGGTTGGCGATTGGCGATTGGGTCCTCGAAAGATTCATTTACCTGGGGTTTCGCCTCTC
ACCGGTAGCTTTAGTACGAGCTGGAATCAGTATGGAGATAAATTTGCAGTCGCAAGTGAG


Am I doing something wrong?

Thanks
Will