Premier test roary

[jorondo1]

Salut, suite à mon dernier courriel, j'essaie cette commande que tu m'avais donnée, j'obtiens cette erreur: Use of uninitialized value in require at /project/def-ilafores/miniconda3/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61.

voici ma commande à partir de l'output prokka roary -p 32 -f out_roary/ -e -n -v \ /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-DICUND-G_KO/*.gff

[jflucier]

je viens de partir ca sour ton compte:

Tue 27 Sep 2022 02:13:16 PM EDT --> [ CCSUDO - ronj2303 ] 
(roary) [ronj2303@ip29-mp2 kofamscan]$ roary -p 32 -f out_roary/ -e -n -v /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/*/*.gff
Use of uninitialized value in require at /project/6047190/miniconda3/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61.

Please cite Roary if you use any of the results it produces:
    Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
    "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
    doi: http://doi.org/10.1093/bioinformatics/btv421
    Pubmed: 26198102

2022/09/27 14:13:43 Output directory created: out_roary/
2022/09/27 14:13:43 Fixing input GFF files
....

L'erreur avec Encode est pas critique.

Ta commande listait un seul gff, jai modifier pour avoir la liste complete des gff: /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan//.gff

La matrice de gene composition sera faite pour toutes les echantillons.

je te reviens lorsque c'est termine.

[jorondo1]

le problème était juste que j'envoyais un seul sample?

[jflucier]

lerreur encode n'etait pas u probleme et roary exec pareil

jai jamais essaye d'exec roary avec un seul echantillon... c'est un peu contraire a son utlisation.

c'est encore en train de rouler:

Tue 27 Sep 2022 02:13:16 PM EDT --> [ CCSUDO - ronj2303 ] 
(roary) [ronj2303@ip29-mp2 kofamscan]$ roary -p 32 -f out_roary/ -e -n -v /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/*/*.gff
Use of uninitialized value in require at /project/6047190/miniconda3/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61.

Please cite Roary if you use any of the results it produces:
    Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
    "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
    doi: http://doi.org/10.1093/bioinformatics/btv421
    Pubmed: 26198102

2022/09/27 14:13:43 Output directory created: out_roary/
2022/09/27 14:13:43 Fixing input GFF files
2022/09/27 15:09:11 Extracting proteins from GFF files
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-DICUND-B_KO/N-1-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-DICUND-G_KO/N-1-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLCOM-G_KO/N-1-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLJUN-B_KO/N-1-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLJUN-G_KO/N-1-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLPIL-G_KO/N-1-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-RACCAN-G_KO/N-1-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-TORTORT-G_KO/N-1-TORTORT-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-DICUND-B_KO/N-2-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-DICUND-G_KO/N-2-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLCOM-B_KO/N-2-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLCOM-G_KO/N-2-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLJUN-B_KO/N-2-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLJUN-G_KO/N-2-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-RACCAN-G_KO/N-2-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-TORTOR-G_KO/N-2-TORTOR-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-3-DICUND-B_KO/N-3-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-3-DICUND-G_KO/N-3-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-3-POLJUN-B_KO/N-3-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-3-POLJUN-G_KO/N-3-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-3-POLPIL-G_KO/N-3-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-3-RACCAN-G_KO/N-3-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-4-DICUND-G_KO/N-4-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-5-DICUND-G_KO/N-5-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-10-POLJUN-B_KO/S-10-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-10-POLJUN-G_KO/S-10-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-10-POLPIL-B_KO/S-10-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-10-POLPIL-G_KO/S-10-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-10-RACCAN-G_KO/S-10-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-11-POLJUN-B_KO/S-11-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-11-POLJUN-G_KO/S-11-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-11-POLPIL-B_KO/S-11-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-11-POLPIL-G_KO/S-11-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-11-RACCAN-G_KO/S-11-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-12-POLJUN-B_KO/S-12-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-12-POLJUN-G_KO/S-12-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-12-POLPIL-B_KO/S-12-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-12-POLPIL-G_KO/S-12-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-12-RACCAN-G_KO/S-12-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-13-POLJUN-B_KO/S-13-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-13-POLJUN-G_KO/S-13-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-13-POLPIL-B_KO/S-13-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-13-POLPIL-G_KO/S-13-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-13-RACCAN-G_KO/S-13-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-14-POLJUN-B_KO/S-14-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-14-POLJUN-G_KO/S-14-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-14-POLPIL-B_KO/S-14-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-14-POLPIL-G_KO/S-14-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-14-RACCAN-G_KO/S-14-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-15-POLJUN-B_KO/S-15-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-15-POLJUN-G_KO/S-15-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-15-POLPIL-B_KO/S-15-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-15-POLPIL-G_KO/S-15-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-15-RACCAN-G_KO/S-15-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-16-POLJUN-G_KO/S-16-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-16-POLPIL-B_KO/S-16-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-16-POLPIL-G_KO/S-16-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-16-RACCAN-G_KO/S-16-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-17-POLJUN-B_KO/S-17-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-17-POLJUN-G_KO/S-17-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-17-POLPIL-B_KO/S-17-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-17-POLPIL-G_KO/S-17-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-17-RACCAN-G_KO/S-17-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-18-POLJUN-B_KO/S-18-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-18-POLJUN-G_KO/S-18-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-18-POLPIL-B_KO/S-18-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-18-POLPIL-G_KO/S-18-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-18-RACCAN-G_KO/S-18-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-19-POLJUN-B_KO/S-19-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-19-POLPIL-B_KO/S-19-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-19-POLPIL-G_KO/S-19-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-DICUND-B_KO/S-1-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-POLCOM-B_KO/S-1-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-POLCOM-G_KO/S-1-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-POLJUN-B_KO/S-1-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-POLJUN-G_KO/S-1-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-POLPIL-B_KO/S-1-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-RACCAN-G_KO/S-1-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-1-RACERI-G_KO/S-1-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-20-POLJUN-B_KO/S-20-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-20-POLJUN-G_KO/S-20-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-20-POLPIL-B_KO/S-20-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-20-POLPIL-G_KO/S-20-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-21-POLJUN-B_KO/S-21-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-21-POLJUN-G_KO/S-21-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-21-POLPIL-G_KO/S-21-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-22-POLJUN-B_KO/S-22-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-22-POLJUN-G_KO/S-22-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-22-POLPIL-B_KO/S-22-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-22-POLPIL-G_KO/S-22-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-23-POLJUN-B_KO/S-23-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-23-POLJUN-G_KO/S-23-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-23-POLPIL-B_KO/S-23-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-23-POLPIL-G_KO/S-23-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-24-POLJUN-B_KO/S-24-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-24-POLJUN-G_KO/S-24-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-24-POLPIL-B_KO/S-24-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-24-POLPIL-G_KO/S-24-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-25-POLJUN-B_KO/S-25-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-25-POLJUN-G_KO/S-25-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-25-POLPIL-B_KO/S-25-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-25-POLPIL-G_KO/S-25-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-26-POLJUN-B_KO/S-26-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-26-POLJUN-G_KO/S-26-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-26-POLPIL-B_KO/S-26-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-26-POLPIL-G_KO/S-26-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-27-POLJUN-B_KO/S-27-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-27-POLPIL-B_KO/S-27-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-27-POLPIL-G_KO/S-27-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-POLCOM-G_KO/S-2-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-POLJUN-B_KO/S-2-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-POLJUN-G_KO/S-2-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-POLPIL-B_KO/S-2-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-POLPIL-G_KO/S-2-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-RACCAN-G_KO/S-2-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-2-RACERI-G_KO/S-2-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-DICUND-B_KO/S-3-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-DICUND-G_KO/S-3-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-POLCOM-B_KO/S-3-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-POLCOM-G_KO/S-3-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-POLJUN-B_KO/S-3-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-POLJUN-G_KO/S-3-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-POLPIL-B_KO/S-3-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-POLPIL-G_KO/S-3-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-RACCAN-G_KO/S-3-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-3-RACERI-G_KO/S-3-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-DICUND-B_KO/S-4-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-DICUND-G_KO/S-4-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-POLCOM-B_KO/S-4-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-POLCOM-G_KO/S-4-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-POLPIL-B_KO/S-4-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-POLPIL-G_KO/S-4-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-RACCAN-G_KO/S-4-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-4-RACERI-G_KO/S-4-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-DICUND-B_KO/S-5-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-DICUND-G_KO/S-5-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-POLCOM-B_KO/S-5-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-POLCOM-G_KO/S-5-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-POLPIL-B_KO/S-5-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-POLPIL-G_KO/S-5-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-RACCAN-G_KO/S-5-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-5-RACERI-G_KO/S-5-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-DICUND-B_KO/S-6-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-DICUND-G_KO/S-6-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-POLCOM-B_KO/S-6-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-POLCOM-G_KO/S-6-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-POLPIL-B_KO/S-6-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-POLPIL-G_KO/S-6-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-RACCAN-G_KO/S-6-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-6-RACERI-G_KO/S-6-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-DICUND-B_KO/S-7-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-DICUND-G_KO/S-7-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-POLCOM-B_KO/S-7-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-POLCOM-G_KO/S-7-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-POLJUN-B_KO/S-7-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-POLJUN-G_KO/S-7-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-POLPIL-B_KO/S-7-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-POLPIL-G_KO/S-7-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-RACCAN-G_KO/S-7-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-7-RACERI-G_KO/S-7-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-DICUND-B_KO/S-8-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-DICUND-G_KO/S-8-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-POLCOM-B_KO/S-8-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-POLCOM-G_KO/S-8-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-POLJUN-B_KO/S-8-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-POLJUN-G_KO/S-8-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-POLPIL-B_KO/S-8-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-POLPIL-G_KO/S-8-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-8-RACCAN-G_KO/S-8-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-DICUND-B_KO/S-9-DICUND-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-DICUND-G_KO/S-9-DICUND-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-POLCOM-B_KO/S-9-POLCOM-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-POLCOM-G_KO/S-9-POLCOM-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-POLJUN-B_KO/S-9-POLJUN-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-POLJUN-G_KO/S-9-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-POLPIL-B_KO/S-9-POLPIL-B.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-POLPIL-G_KO/S-9-POLPIL-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-RACCAN-G_KO/S-9-RACCAN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/S-9-RACERI-G_KO/S-9-RACERI-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/W-1-POLJUN-G_KO/W-1-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/W-1-TORTOR-G_KO/W-1-TORTOR-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/W-2-POLJUN-G_KO/W-2-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/W-2-TORTOR-G_KO/W-2-TORTOR-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/W-3-POLJUN-G_KO/W-3-POLJUN-G.gff
Extracting proteins from /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/W-4-POLJUN-G_KO/W-4-POLJUN-G.gff
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:

  Tange, O. (2022, July 22). GNU Parallel 20220722 ('Roe vs Wade').
  Zenodo. https://doi.org/10.5281/zenodo.6891516

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#citation-notice

To silence this citation notice: run 'parallel --citation' once.

Combine proteins into a single file
Iteratively run cd-hit
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:

  Tange, O. (2022, July 22). GNU Parallel 20220722 ('Roe vs Wade').
  Zenodo. https://doi.org/10.5281/zenodo.6891516

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#citation-notice

To silence this citation notice: run 'parallel --citation' once.

[jflucier]

hmm va falloir que je check pour optimiser ca... jamais essayer de tournerr roary sur autant de samples.

ca pas fini encore.

|09:49:17|jflucier@ip29:[~]> ps aux | grep -e perl
ronj2303   360  0.0  0.0 146720 16224 ?        S    Sep29   2:03 perl /project/def-ilafores/miniconda3/envs/roary/bin/parallel --gnu -j 32
jflucier 32077  0.0  0.0  12752   912 pts/14   S+   09:50   0:00 grep --color=auto -e perl
ronj2303 44883  0.7  0.4 1303972 1157664 ?     S    Sep27  65:57 perl /project/def-ilafores/miniconda3/envs/roary/bin/roary -p 32 -f out_roary/ -e -n -v /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-DICUND-B_KO/N-1-DICUND-B.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-DICUND-G_KO/N-1-DICUND-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLCOM-G_KO/N-1-POLCOM-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLJUN-B_KO/N-1-POLJUN-B.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLJUN-G_KO/N-1-POLJUN-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-POLPIL-G_KO/N-1-POLPIL-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-RACCAN-G_KO/N-1-RACCAN-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-1-TORTORT-G_KO/N-1-TORTORT-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-DICUND-B_KO/N-2-DICUND-B.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-DICUND-G_KO/N-2-DICUND-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLCOM-B_KO/N-2-POLCOM-B.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLCOM-G_KO/N-2-POLCOM-G.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLJUN-B_KO/N-2-POLJUN-B.gff /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/N-2-POLJUN-G_KO/N-....

[jorondo1]

oh daym! Étrange. Même si c'est beaucoup de samples, c'est pas beaucoup de données, 3-4 bins par sample en moyenne seulement... tiens-moi au courant

[jflucier]

je prend les gff du dossier /ip29/ilafores_group/analysis/20220825_boreal_moss/kofamscan/

c'est bien des gff genere a partir des bins de chacun des echantillons?

[jorondo1]

oui exact

[jflucier]

check ca:

https://github.com/sanger-pathogens/Roary/issues/479

[jflucier]

de ce que je comprend roary doit etre exec sur un meme espece. Ca pas lair de bien aller lorsque c'est pas possible de clusterer les proteines ensemble.

dans les echantillons, est-ce possible de les grouper? Genre:

Tue 04 Oct 2022 02:40:53 PM EDT --> [ CCSUDO - ronj2303 ] 
[ronj2303@ip29-mp2 kofamscan]$ ls -d *POLCOM*
N-1-POLCOM-G_KO  N-2-POLCOM-G_KO  S-1-POLCOM-G_KO  S-3-POLCOM-B_KO  S-4-POLCOM-B_KO  S-5-POLCOM-B_KO  S-6-POLCOM-B_KO  S-7-POLCOM-B_KO  S-8-POLCOM-B_KO  S-9-POLCOM-B_KO
N-2-POLCOM-B_KO  S-1-POLCOM-B_KO  S-2-POLCOM-G_KO  S-3-POLCOM-G_KO  S-4-POLCOM-G_KO  S-5-POLCOM-G_KO  S-6-POLCOM-G_KO  S-7-POLCOM-G_KO  S-8-POLCOM-G_KO  S-9-POLCOM-G_KO

Tue 04 Oct 2022 02:41:04 PM EDT --> [ CCSUDO - ronj2303 ] 
[ronj2303@ip29-mp2 kofamscan]$ ls -d *DICUND*
N-1-DICUND-B_KO  N-2-DICUND-B_KO  N-3-DICUND-B_KO  N-4-DICUND-G_KO  S-1-DICUND-B_KO  S-3-DICUND-G_KO  S-4-DICUND-G_KO  S-5-DICUND-G_KO  S-6-DICUND-G_KO  S-7-DICUND-G_KO  S-8-DICUND-G_KO  S-9-DICUND-G_KO
N-1-DICUND-G_KO  N-2-DICUND-G_KO  N-3-DICUND-G_KO  N-5-DICUND-G_KO  S-3-DICUND-B_KO  S-4-DICUND-B_KO  S-5-DICUND-B_KO  S-6-DICUND-B_KO  S-7-DICUND-B_KO  S-8-DICUND-B_KO  S-9-DICUND-B_KO

Tue 04 Oct 2022 02:41:12 PM EDT --> [ CCSUDO - ronj2303 ] 
[ronj2303@ip29-mp2 kofamscan]$ ls -d *POLJUN*
N-1-POLJUN-B_KO  N-3-POLJUN-B_KO   S-11-POLJUN-B_KO  S-13-POLJUN-B_KO  S-15-POLJUN-B_KO  S-17-POLJUN-G_KO  S-1-POLJUN-B_KO   S-21-POLJUN-B_KO  S-23-POLJUN-B_KO  S-25-POLJUN-B_KO  S-27-POLJUN-B_KO  S-3-POLJUN-G_KO  S-8-POLJUN-G_KO  W-2-POLJUN-G_KO
N-1-POLJUN-G_KO  N-3-POLJUN-G_KO   S-11-POLJUN-G_KO  S-13-POLJUN-G_KO  S-15-POLJUN-G_KO  S-18-POLJUN-B_KO  S-1-POLJUN-G_KO   S-21-POLJUN-G_KO  S-23-POLJUN-G_KO  S-25-POLJUN-G_KO  S-2-POLJUN-B_KO   S-7-POLJUN-B_KO  S-9-POLJUN-B_KO  W-3-POLJUN-G_KO
N-2-POLJUN-B_KO  S-10-POLJUN-B_KO  S-12-POLJUN-B_KO  S-14-POLJUN-B_KO  S-16-POLJUN-G_KO  S-18-POLJUN-G_KO  S-20-POLJUN-B_KO  S-22-POLJUN-B_KO  S-24-POLJUN-B_KO  S-26-POLJUN-B_KO  S-2-POLJUN-G_KO   S-7-POLJUN-G_KO  S-9-POLJUN-G_KO  W-4-POLJUN-G_KO
N-2-POLJUN-G_KO  S-10-POLJUN-G_KO  S-12-POLJUN-G_KO  S-14-POLJUN-G_KO  S-17-POLJUN-B_KO  S-19-POLJUN-B_KO  S-20-POLJUN-G_KO  S-22-POLJUN-G_KO  S-24-POLJUN-G_KO  S-26-POLJUN-G_KO  S-3-POLJUN-B_KO   S-8-POLJUN-B_KO  W-1-POLJUN-G_KO

[jorondo1]

Ok, je ne pense pas que Roary soit adapté à ce qu'on fait, étant donné qu'on travaille avec des métagénomes. On va tester Metabolic voir quel genre d'output on obtient visuellement. Kofamscan aussi est intéressant pour son heatmap métabolique par sample, je vais comparer les deux et je verrai lequel on intègre au pipeline.