gff file format problem while running m2m recon

[gpchoupichou]

Hello, I have a problem running the following command : m2m recon -g rocks -o rocks_m2m -c 16 Here is the error message :

######### Running metabolic network reconstruction with Pathway Tools #########
---------- Launching mpwt ----------
No region feature in the GFF file of rocks_bin_231_1, GFF file must have region features.

and here is an example of my gff file (obtained with prokka) :

##gff-version 3
##sequence-region c_000000064644 1 1078188
##sequence-region c_000000108022 1 72333
##sequence-region c_000000177873 1 343976
##sequence-region c_000000291080 1 70581
##sequence-region c_000000322418 1 191404
##sequence-region c_000000063443 1 369988
##sequence-region c_000000303010 1 359558
##sequence-region c_000000318942 1 41289
##sequence-region c_000000318773 1 77515
##sequence-region c_000000223418 1 76416
##sequence-region c_000000203556 1 36017
##sequence-region c_000000344245 1 16104
##sequence-region c_000000367754 1 171665
##sequence-region c_000000255903 1 128623
##sequence-region c_000000275449 1 42783
##sequence-region c_000000354647 1 95858
##sequence-region c_000000024095 1 45991
##sequence-region c_000000372217 1 178286
##sequence-region c_000000107681 1 114885
##sequence-region c_000000035827 1 97699
##sequence-region c_000000026743 1 214901
##sequence-region c_000000063357 1 165766
##sequence-region c_000000013580 1 89699
##sequence-region c_000000299742 1 96705
##sequence-region c_000000021783 1 29717
##sequence-region c_000000429765 1 46987
##sequence-region c_000000271007 1 23297
##sequence-region c_000000291991 1 29199
##sequence-region c_000000297940 1 11292
c_000000064644  Prodigal:002006 CDS     137     1213    .       -       0       ID=KJGKFCMM_00001;Name=mreB_1;gene=mreB_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:A0A0H3C7V4;locus_tag=KJGKFCMM_00001;product=Cell shape-determining protein MreB
c_000000064644  Prodigal:002006 CDS     1420    2079    .       -       0       ID=KJGKFCMM_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=KJGKFCMM_00002;product=hypothetical protein
c_000000064644  Prodigal:002006 CDS     2445    3521    .       -       0       ID=KJGKFCMM_00003;eC_number=5.2.1.8;Name=surA_1;gene=surA_1;inference=ab initio prediction:Prodigal:002006,protein motif:HAMAP:MF_01183;locus_tag=KJGKFCMM_00003;product=Chaperone SurA
c_000000064644  Prodigal:002006 CDS     3621    7397    .       -       0       ID=KJGKFCMM_00004;eC_number=3.6.4.-;Name=mfd;gene=mfd;inference=ab initio prediction:Prodigal:002006,protein motif:HAMAP:MF_00969;locus_tag=KJGKFCMM_00004;product=Transcription-repair-coupling factor
c_000000064644  Prodigal:002006 CDS     7642    8118    .       -       0       ID=KJGKFCMM_00005;Name=hldE_1;db_xref=COG:COG2870;gene=hldE_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P76658;locus_tag=KJGKFCMM_00005;product=Bifunctional protein HldE
c_000000064644  Prodigal:002006 CDS     8330    9919    .       +       0       ID=KJGKFCMM_00006;eC_number=6.1.1.6;Name=lysU;db_xref=COG:COG1190;gene=lysU;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A8N5;locus_tag=KJGKFCMM_00006;product=Lysine--tRNA ligase%2C heat inducible
c_000000064644  Prodigal:002006 CDS     10088   10498   .       -       0       ID=KJGKFCMM_00007;inference=ab initio prediction:Prodigal:002006;locus_tag=KJGKFCMM_00007;product=hypothetical protein
c_000000064644  Prodigal:002006 CDS     10679   11710   .       -       0       ID=KJGKFCMM_00008;db_xref=COG:COG4447;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q8DI95;locus_tag=KJGKFCMM_00008;product=Ycf48-like protein

I tried to convert to gbk but the taxonomy was missing and it was still not working. Do you have any idea how I could fix this problem ? Thanks a lot, Guillaume