Odgi squeeze doesn't recognize my GFAv1 files

[MarionPerrier]

Hi!

I used PGGB to build a pangenome graphs of 15 assemblies. The PGGB pipeline splits the assemblies in communities, resulting in several GFA output for each communities. I would like to use odgi squeeze to combine my GFA graphs into a single one for further processing with VG.

Here is my command line:

odgi squeeze -f combined_pg.fa.gz.community.0.smoothxg.gfa -f combined_pg.fa.gz.community.0.smoothxg.gfa -f combined_pg.fa.gz.community.1.smoothxg.gfa -f combined_pg.fa.gz.community.2.smoothxg.gfa -f combined_pg.fa.gz.community.3.smoothxg.gfa -f combined_pg.fa.gz.community.4.smoothxg.gfa -f combined_pg.fa.gz.community.5.smoothxg.gfa -f combined_pg.fa.gz.community.6.smoothxg.gfa -f combined_pg.fa.gz.community.7.smoothxg.gfa -f combined_pg.fa.gz.community.8.smoothxg.gfa -f combined_pg.fa.gz.community.9.smoothxg.gfa -t 12 -o final.og

Here is the error:

[odgi::squeeze] error: the given file "H        VN:Z:1.0" does not exist. Please specify an existing input file in ODGI format via -i=[FILE], --idx=[FILE].

If I replace the "-f" by "-i", I then get an error "Flag could not be matched: 'i'"

What am I doing wrong? My GFA files are indeed GFAv1.

Here is an example of the smallest of them:

(odgi) [fu46von@node009 smoothxg]$ cat combined_corrected_Chr1and4.fa.gz.community.9.smoothxg.gfa
H       VN:Z:1.0
S       1       ACATAGTGTATTCCAACGCCCTTTTAACACCTTTTAAATACTAACATAAAGCCCTTTGTCGACCGCGATTAATAGTCAAGAACTACTAGTGTTAATCCTTAATAGCTACTTTAGGATTAGCATGGTTCAGGATAAACCTCTCTAAAGGGGGGGGGTAGTTATCATATACTCAGAATAATATAAGCCTAGCAAGCCACTAGTGGCAAGCCCCCTCTTACTTAGGTAATTATATACCTGATTCTGAATGTACTTAGTAGAAATAGGAGTTCTAAATAGCTTAGGGGAGACCAAGCAGTTTGTTCTAATCATTAATATATATACATTTTCACTAATACATCTATACATCCCTAAAACCCAGTATTCCTATCTATAGCCGCAGCCTAG
L       1       +       2       +       0M
S       2       TCGCCGTCGCATCGCTGGCTAGGACCCCCTAGGTCAATTACCTCCGATCGCCTTACAACTAAATATATATTATAA
L       2       +       4       +       0M
L       2       +       3       +       0M
S       3       A
L       3       +       5       +       0M
S       4       G
L       4       +       5       +       0M
S       5       TATTTATAGCAGGAGCTAATTATAGCTTAATTAAGTAATAGTTTTATCTATAGCTTAGAGCAGAAGGTCTAATATATAGCCTTATTAGTACTATTATATATTTCTATATTAGGTAGAATAGGTTTTAGTCTCTTTATTAGGTCTTCTA
L       5       +       7       +       0M
L       5       +       6       +       0M
S       6       A
L       6       +       8       +       0M
S       7       T
L       7       +       8       +       0M
S       8       AGAGGTAGTAGTTAGGATGGGTGTAAAGGGAGTTACTTAGGGAGTAAGTATTACTACTATAGTAGTAGTAGTAGTTACTTATTATTCTTTAATGTCACGGTGCTGCCACAGACAGGAGTTAGTGTTACTAAGAAGGAATTATGTGACTCTAGGAATATCTTCACTATATAATCCTGCAATCTATTTAGAAGTCTTTAAGCTATGTCCTGTCTATAGAGCCTGCCTGTACTAGTTTACCCTATAATTAGAATAAATAGATATAGATTCCTATAGCCAGCCTAAGTGTTAACTACCTTATTAACCTGTTTCTGTTTACCTATAACCCTGTATCTTAATATTATATAGCTCCACCCTTGGAGTTAACACTGTCAGAATACCCACCCCTCTGCCCCTATTCCTACCTAGTGATCCTAAAGAGTTCTCTAAGCATGTTGCTAAACATGGTACTAAATAGTATAAATACTGCCACCTGGCATATGAGTACATCCAGAAGGCCAAATTGACTATCAATGAACCAGACCAACCAGACCAACCAGACCAACCAGACT
L       8       +       9       +       0M
S       9       AACC
P       Sample5#0#scaffold_159     2+,4+,5+,7+,8+  *
P       Sample1#0#scaffold_27       1+,2+,3+,5+,6+,8+,9+    *

Odgi has been installed using conda, and the version is v0.8.4-0-g3f59d596

[subwaystation]

So you need to provide a file with -f which contains all the files you want to squeeze together. For example my_graphs.txt:

combined_pg.fa.gz.community.0.smoothxg.gfa
combined_pg.fa.gz.community.0.smoothxg.gfa
combined_pg.fa.gz.community.1.smoothxg.gfa
combined_pg.fa.gz.community.2.smoothxg.gfa
combined_pg.fa.gz.community.3.smoothxg.gfa
combined_pg.fa.gz.community.4.smoothxg.gfa
combined_pg.fa.gz.community.5.smoothxg.gfa
combined_pg.fa.gz.community.6.smoothxg.gfa
combined_pg.fa.gz.community.7.smoothxg.gfa
combined_pg.fa.gz.community.8.smoothxg.gfa
combined_pg.fa.gz.community.9.smoothxg.gfa

[MarionPerrier]

Oh ok! It works like a charm now. Thank you