[MUMmer-help] Error when running mapview with cds

[Deepak K. <dee...@an...>]

Dear Mummer Users,


I am trying to run mummer on 2 phage genomes and looking to generate the mapview figure. I have generated the coords file for the 2 phages (attached), and I also prepared a cds file for the reference (attached). And, then ran command:


./mapview -n 1 -f pdf -p  mapview ref_qry.coords KP010413_1.cds


but I keep getting error:

 ERROR in the input files ! The reference seq ID can't be found in GFF files !
      The first column in the GFF file should be the ID of the reference seq.
      The alignments file should provide the same info in the column before the last one.

      Here are some example records for the GFF file:

      gnl|FlyBase|X    Dmel3    initial-exon    2155    2413    .    -    .    X_CG3038.1
      gnl|FlyBase|X    Dmel3    last-exon    1182    2077    .    -    .    X_CG3038.1
      ...
      The fields are :
      <seq_ID> <source> <exon type> <start> <end> <score> <strand> <frame> <gene_name>




Please let me know what is the issue here; I would really appreciate.


Thanks,

DK


________________________________
From: Deepak Kumar
Sent: Monday, February 11, 2019 5:10 PM
To: mum...@li...
Subject: Error when running mapview with cds


Dear Mummer Users,


I am trying to run mummer on 2 phage genomes and looking to generate the mapview figure. I have generated the coords file for the 2 phages (attached), and I also prepared a cds file for the reference (attached). And, then ran command:


./mapview -n 1 -f pdf -p  mapview ref_qry.coords KP010413_1.cds


but I keep getting error:

 ERROR in the input files ! The reference seq ID can't be found in GFF files !
      The first column in the GFF file should be the ID of the reference seq.
      The alignments file should provide the same info in the column before the last one.

      Here are some example records for the GFF file:

      gnl|FlyBase|X    Dmel3    initial-exon    2155    2413    .    -    .    X_CG3038.1
      gnl|FlyBase|X    Dmel3    last-exon    1182    2077    .    -    .    X_CG3038.1
      ...
      The fields are :
      <seq_ID> <source> <exon type> <start> <end> <score> <strand> <frame> <gene_name>




Please let me know what is the issue here; I would really appreciate.


Thanks,

DK