run new_species.pl error

[shiyi-pan]

Hi, I want to use this vrey good software to predict genes. But I meet a problem when I train the module. here is my code :

$AUGUSTUS/scripts/new_species.pl --species=for_bad_genes_removing --AUGUSTUS_CONFIG_PATH=/ds3512/home/panyp/genome_assess/augustus-3.3.3/config

here is the error:

Directory /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species is not writable. Cannot create new species. Please check whether AUGUSTUS_CONFIG_PATH is set, correctly.

Was I set the wrong species ? coluld you give me some advise ? Thank you very much.

[MarioStanke]

What does ls -la /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species return (only the line from the directory .)?

[shiyi-pan]

thank you for your reply,here is the result of "ls" command, I run this in my home directory:

total 448 drwxrwxr-x 112 panyp panyp 4096 Oct 20 17:10 . drwxrwxr-x 7 panyp panyp 4096 May 22 2019 .. drwxrwxr-x 2 panyp panyp 4096 May 22 2019 adorsata drwxrwxr-x 2 panyp panyp 4096 May 22 2019 aedes drwxrwxr-x 2 panyp panyp 4096 May 22 2019 amphimedon drwxrwxr-x 2 panyp panyp 4096 May 22 2019 ancylostoma_ceylanicum drwxrwxr-x 2 panyp panyp 4096 May 22 2019 anidulans drwxrwxr-x 2 panyp panyp 4096 May 22 2019 arabidopsis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 aspergillus_fumigatus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 aspergillus_nidulans drwxrwxr-x 2 panyp panyp 4096 May 22 2019 aspergillus_oryzae drwxrwxr-x 2 panyp panyp 4096 May 22 2019 aspergillus_terreus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 bombus_impatiens1 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 bombus_terrestris2 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 botrytis_cinerea drwxrwxr-x 2 panyp panyp 4096 May 22 2019 b_pseudomallei drwxrwxr-x 2 panyp panyp 4096 May 22 2019 brugia drwxrwxr-x 2 panyp panyp 4096 May 22 2019 cacao drwxrwxr-x 2 panyp panyp 4096 May 22 2019 caenorhabditis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 camponotus_floridanus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 candida_albicans drwxrwxr-x 2 panyp panyp 4096 May 22 2019 candida_guilliermondii drwxrwxr-x 2 panyp panyp 4096 May 22 2019 candida_tropicalis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 c_elegans_trsk drwxrwxr-x 2 panyp panyp 4096 May 22 2019 chaetomium_globosum drwxrwxr-x 2 panyp panyp 4096 May 22 2019 chicken drwxrwxr-x 2 panyp panyp 4096 May 22 2019 chiloscyllium drwxrwxr-x 2 panyp panyp 4096 May 22 2019 chlamy2011 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 chlamydomonas drwxrwxr-x 2 panyp panyp 4096 May 22 2019 chlorella drwxrwxr-x 2 panyp panyp 4096 May 22 2019 ciona drwxrwxr-x 2 panyp panyp 4096 May 22 2019 coccidioides_immitis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 Conidiobolus_coronatus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 coprinus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 coprinus_cinereus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 coyote_tobacco drwxrwxr-x 2 panyp panyp 4096 May 22 2019 cryptococcus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 cryptococcus_neoformans_gattii drwxrwxr-x 2 panyp panyp 4096 May 22 2019 cryptococcus_neoformans_neoformans_B drwxrwxr-x 2 panyp panyp 4096 May 22 2019 cryptococcus_neoformans_neoformans_JEC21 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 culex drwxrwxr-x 2 panyp panyp 4096 May 22 2019 debaryomyces_hansenii drwxrwxr-x 2 panyp panyp 4096 May 22 2019 E_coli_K12 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 elephant_shark drwxrwxr-x 2 panyp panyp 4096 May 22 2019 encephalitozoon_cuniculi_GB drwxrwxr-x 2 panyp panyp 4096 May 22 2019 eremothecium_gossypii drwxrwxr-x 2 panyp panyp 4096 May 22 2019 fly drwxrwxr-x 2 panyp panyp 4096 May 22 2019 fly_exp drwxrwxr-x 2 panyp panyp 4096 Oct 5 16:42 for_bad_genes_removing drwxrwxr-x 2 panyp panyp 4096 May 22 2019 fusarium drwxrwxr-x 2 panyp panyp 4096 May 22 2019 fusarium_graminearum drwxrwxr-x 2 panyp panyp 4096 May 22 2019 galdieria drwxrwxr-x 2 panyp panyp 4096 Sep 13 2019 generic drwxrwxr-x 2 panyp panyp 4096 May 22 2019 heliconius_melpomene1 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 histoplasma drwxrwxr-x 2 panyp panyp 4096 May 22 2019 histoplasma_capsulatum drwxrwxr-x 2 panyp panyp 4096 May 22 2019 honeybee1 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 human drwxrwxr-x 2 panyp panyp 4096 May 22 2019 japaneselamprey drwxrwxr-x 2 panyp panyp 4096 May 22 2019 kluyveromyces_lactis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 laccaria_bicolor drwxrwxr-x 2 panyp panyp 4096 May 22 2019 leishmania_tarentolae drwxrwxr-x 2 panyp panyp 4096 May 22 2019 lodderomyces_elongisporus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 magnaporthe_grisea drwxrwxr-x 2 panyp panyp 4096 May 22 2019 maize drwxrwxr-x 2 panyp panyp 4096 May 22 2019 maize5 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 mnemiopsis_leidyi drwxrwxr-x 2 panyp panyp 4096 May 22 2019 nasonia drwxrwxr-x 2 panyp panyp 4096 May 22 2019 nematostella_vectensis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 neurospora drwxrwxr-x 2 panyp panyp 4096 May 22 2019 neurospora_crassa drwxrwxr-x 2 panyp panyp 4096 May 22 2019 parasteatoda drwxrwxr-x 2 panyp panyp 4096 May 22 2019 pchrysosporium drwxrwxr-x 2 panyp panyp 4096 May 22 2019 pea_aphid drwxrwxr-x 2 panyp panyp 4096 May 22 2019 pfalciparum drwxrwxr-x 2 panyp panyp 4096 May 22 2019 phanerochaete_chrysosporium drwxrwxr-x 2 panyp panyp 4096 May 22 2019 pichia_stipitis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 pisaster drwxrwxr-x 2 panyp panyp 4096 May 22 2019 pneumocystis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 rhincodon drwxrwxr-x 2 panyp panyp 4096 May 22 2019 rhizopus_oryzae drwxrwxr-x 2 panyp panyp 4096 May 22 2019 rhodnius drwxrwxr-x 2 panyp panyp 4096 May 22 2019 rice drwxrwxr-x 2 panyp panyp 4096 May 22 2019 saccharomyces drwxrwxr-x 2 panyp panyp 4096 May 22 2019 saccharomyces_cerevisiae_rm11-1a_1 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 saccharomyces_cerevisiae_S288C drwxrwxr-x 2 panyp panyp 4096 May 22 2019 s_aureus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 schistosoma drwxrwxr-x 2 panyp panyp 4096 May 22 2019 schistosoma2 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 schizosaccharomyces_pombe drwxrwxr-x 2 panyp panyp 4096 May 22 2019 scyliorhinus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 sealamprey drwxrwxr-x 2 panyp panyp 4096 Oct 20 17:11 soybean drwxrwxr-x 2 panyp panyp 4096 May 22 2019 s_pneumoniae drwxrwxr-x 2 panyp panyp 4096 May 22 2019 strongylocentrotus_purpuratus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 sulfolobus_solfataricus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 template_prokaryotic drwxrwxr-x 2 panyp panyp 4096 May 22 2019 tetrahymena drwxrwxr-x 2 panyp panyp 4096 May 22 2019 thermoanaerobacter_tengcongensis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 tomato drwxrwxr-x 2 panyp panyp 4096 May 22 2019 toxoplasma drwxrwxr-x 2 panyp panyp 4096 May 22 2019 tribolium2012 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 trichinella drwxrwxr-x 2 panyp panyp 4096 May 22 2019 ustilago drwxrwxr-x 2 panyp panyp 4096 May 22 2019 ustilago_maydis drwxrwxr-x 2 panyp panyp 4096 May 22 2019 verticillium_albo_atrum1 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 verticillium_longisporum1 drwxrwxr-x 2 panyp panyp 4096 May 22 2019 volvox drwxrwxr-x 2 panyp panyp 4096 May 22 2019 wheat drwxrwxr-x 2 panyp panyp 4096 May 22 2019 Xipophorus_maculatus drwxrwxr-x 2 panyp panyp 4096 May 22 2019 yarrowia_lipolytica drwxrwxr-x 2 panyp panyp 4096 May 22 2019 zebrafish

[MarioStanke]

OK. You already have a directory with that name. Maybe that is it. Can you

rm -r /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species/for_bad_genes_removing
mkdir /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species/for_bad_genes_removing
rmdir /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species/for_bad_genes_removing

as the same user as and from the same directory where you execute new_species.pl?

[shiyi-pan]

Hi,thank you for your reply. I find a situation. When I run the script in my login node, it works well, but submit to compute node using qsub, it works wrong.

here is the log I run the script in my login node:

Will create parameters for a EUKARYOTIC species! creating directory /ds3512/home/panyp/genome_assess/augustus-3.3.3/config/species/for_bad_genes_removing/ ... creating /ds3512/home/panyp/genome_assess/augustus-3.3.3/config/species/for_bad_genes_removing/for_bad_genes_removing_parameters.cfg ... creating /ds3512/home/panyp/genome_assess/augustus-3.3.3/config/species/for_bad_genes_removing/for_bad_genes_removing_weightmatrix.txt ... creating /ds3512/home/panyp/genome_assess/augustus-3.3.3/config/species/for_bad_genes_removing/for_bad_genes_removing_metapars.cfg ... The necessary files for training for_bad_genes_removing have been created. Now, either run etraining or optimize_parameters.pl with --species=for_bad_genes_removing. etraining quickly estimates the parameters from a file with training genes. optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.