peguerin (ffaed86b) at 04 Sep 13:25
update version
peguerin (9843a6a6) at 04 Sep 13:25
add ncbi taxon root id argument
peguerin (5962c60a) at 04 Sep 13:24
add argument to set rootaxon value
peguerin (3efb13f6) at 22 Jun 15:16
mon dernier commit
names.dmp:3416120:2839645 | ANK:collector:H.Duman:10209 | | isotype |
names.dmp:3416121:2839645 | GAZI:collector:H.Duman:10209 | | holotype |
names.dmp:3416122:2839645 | HUB:collector:H.Duman:10209 | | isotype |
causing ecotag to fail
I have some species name indicated as faulty format if there is more than Genus_species for example Genus_species_subspecies (or even Genus_sp_cf_species for when there is a possible new undescribed species)
>RBM2_194; species_name=Syngnathus_typhle_rondeleti ; faulty species name format Syngnathus_typhle_rondeleti
CCCCTAATATCTCATAAATTTAAGTAAAACACCTGAAAAATTAAGGGGAGGCAAGTCGTA
A
It needs to be corrected to allow such cases in an accepted format
Example with the csv for curation
current_name;ncbi_name;genus;family;ncbi_rank;method
Albula forsteri;Albula argentea;Albula;Albulidae;species;NCBI synonym score=1.0
Albula forsteri;Albula argentea;Albula;Albulidae;species;NCBI synonym score=1.0
Albula forsteri;Albula argentea;Albula;Albulidae;species;NCBI synonym score=1.0
Amphiprion fuscocaudatus;NA;Amphiprion;Pomacentridae;genus;Catalogue of Life
Atherinomorus lineatus;NA;Atherinomorus;Atherinidae;genus;Catalogue of Life
Haemulon chrysargyreum;Brachygenys chrysargyreum;Brachygenys;Haemulidae;species;NCBI synonym score=1.0
Haemulon chrysargyreum;Brachygenys chrysargyreum;Brachygenys;Haemulidae;species;NCBI synonym score=1.0
Canthigaster epilampra;NA;Canthigaster;Tetraodontidae;genus;Catalogue of Life
Distichodus perspicillatus;NA;Distichodus;Distichodontidae;genus;Catalogue of Life
Distichodus perspicillatus;NA;Distichodus;Distichodontidae;genus;Catalogue of Life
Hirundichthys rondeleti;Hirundichthys rondeletii;Hirundichthys;Exocoetidae;species;NCBI synonym score=0.9565217391304348
Haemulon chrysargyreum;Brachygenys chrysargyreum;Brachygenys;Haemulidae;species;NCBI synonym score=1.0
Hyporhamphus melanopterus;NA;Hyporhamphus;Hemiramphidae;genus;Catalogue of Life
Haemulopsis corvinaeformis;Pomadasys corvinaeformis;Pomadasys;Haemulidae;species;NCBI synonym score=1.0
Neoglyphidodon crossi;NA;Neoglyphidodon;Pomacentridae;genus;Catalogue of Life
Neoglyphidodon crossi;NA;Neoglyphidodon;Pomacentridae;genus;Catalogue of Life
Neoploactis tridorsalis;NA;NA;Aploactinidae;family;Catalogue of Life
Ophidion barbatum;NA;Ophidion;Ophidiidae;genus;Catalogue of Life
Ostorhinchus monospilus;NA;Ostorhinchus;Apogonidae;genus;Catalogue of Life
Ostorhinchus monospilus;NA;Ostorhinchus;Apogonidae;genus;Catalogue of Life
Cynoponticus savanna;NA;Cynoponticus;Muraenesocidae;genus;Catalogue of Life
Pseudanthias randali;Pseudanthias randalli;Pseudanthias;Serranidae;species;NCBI synonym score=0.95
Pseudanthias randali;Pseudanthias randalli;Pseudanthias;Serranidae;species;NCBI synonym score=0.95
Pseudanthias randali;Pseudanthias randalli;Pseudanthias;Serranidae;species;NCBI synonym score=0.95
Pseudanthias randali;Pseudanthias randalli;Pseudanthias;Serranidae;species;NCBI synonym score=0.95
Pseudanthias randali;Pseudanthias randalli;Pseudanthias;Serranidae;species;NCBI synonym score=0.95
Pseudanthias randali;Pseudanthias randalli;Pseudanthias;Serranidae;species;NCBI synonym score=0.95
Rhinobatos sainsburyi;NA;Rhinobatos;Rhinobatidae;genus;Catalogue of Life
Aspitrigla cuculus;Chelidonichthys cuculus;Chelidonichthys;Triglidae;species;NCBI synonym score=1.0
Aspitrigla cuculus;Chelidonichthys cuculus;Chelidonichthys;Triglidae;species;NCBI synonym score=1.0
Carcharhinus taurus;Carcharhinus cautus;Carcharhinus;Carcharhinidae;species;NCBI synonym score=0.8947368421052632
Glaucostegus cemicullus;Glaucostegus cemiculus;Glaucostegus;Glaucostegidae;species;NCBI synonym score=0.9565217391304348
Glaucostegus cemicullus;Glaucostegus cemiculus;Glaucostegus;Glaucostegidae;species;NCBI synonym score=0.9565217391304348
Glaucostegus cemicullus;Glaucostegus cemiculus;Glaucostegus;Glaucostegidae;species;NCBI synonym score=0.9565217391304348
Glaucostegus cemicullus;Glaucostegus cemiculus;Glaucostegus;Glaucostegidae;species;NCBI synonym score=0.9565217391304348
Gobius ater;NA;Gobius;Gobiidae;genus;Catalogue of Life
Ophidion rochei;NA;Ophidion;Ophidiidae;genus;NA
Ophidion rochei;NA;Ophidion;Ophidiidae;genus;NA
and the customtaxonomy names.dmp
10000000 | Amphiprion fuscocaudatus | | scientific name |
10000001 | Atherinomorus lineatus | | scientific name |
10000002 | Canthigaster epilampra | | scientific name |
10000003 | Distichodus perspicillatus | | scientific name |
10000004 | Distichodus perspicillatus | | scientific name |
10000005 | Hyporhamphus melanopterus | | scientific name |
10000006 | Neoglyphidodon crossi | | scientific name |
10000007 | Neoglyphidodon crossi | | scientific name |
10000008 | Ophidion barbatum | | scientific name |
10000009 | Ostorhinchus monospilus | | scientific name |
10000010 | Ostorhinchus monospilus | | scientific name |
10000011 | Cynoponticus savanna | | scientific name |
10000012 | Rhinobatos sainsburyi | | scientific name |
10000013 | Gobius ater | | scientific name |
10000014 | Ophidion rochei | | scientific name |
10000015 | Ophidion rochei | | scientific name |
il faut mettre à jour les données test car les runs sont toujours fausses
c'est fait
Il y a une erreur au tout début de la pipeline.
Au moment de merger les reads en utilisant la commande illuminapaired, les fichiers se créent bien mais l'opération s'arrête puis efface les fichiers car ils seraient 'corrupted'. Donc la pipeline s'arrête.
J'ai essayé en lançant la pipeline globale, puis uniquement l'étape 02_ pour un résultat semblable.
Error in rule illuminapairedend:
[Tue Jun 2 12:54:49 2020]
Error in rule illuminapairedend:
[Tue Jun 2 12:54:49 2020]
[Tue Jun 2 12:54:49 2020]
Removing output files of failed job illuminapairedend since they might be corrupted:
01_illuminapairedend/191017_SN234_A_L001_AIMI-148.fastq
bug soit en lien avec le fichier soit en lien avec singulairity
S'inspirer de cette présentation
https://github.com/ifremer-bioinformatics/samba
Le wiki est à refaire/mettre à jour entierement
get started/quick start: https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home#get-started
installation instruction : https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home#installation
Now prepare_spygen have its own wiki page:
https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/prepare_spygen_data