ó uŸbc@€s‡ddlmZddlZddlmZmZmZddlZddlm Z ddl m Z m Z m Z ddlmZddlmZddlmZmZmZmZmZmZee jƒZd Zd Zd ed Zd ZdZdZ ddgZ!dZ"dZ#e$e$d„Z%e$d„Z&e$d„Z'd„Z(d„Z)e$d„Z*d„Z+d„Z,d„Z-d„Z.d„Z/dS(iÿÿÿÿ(twith_statementN(tjointdirnametrealpath(tdownload_unpack_compressed_tar(t reportingtqconfigtqutils(tbusco(t get_logger(tdownload_blast_binariest run_parallelt compile_tooltget_dir_for_downloadtcheck_prev_compilation_failedtget_blast_fpaths3.2.3s3.3s?http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-s.tar.gzs@https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gzs=https://busco-archive.ezlab.org/v3/datasets/fungi_odb9.tar.gzsAhttps://busco-archive.ezlab.org/v3/datasets/eukaryota_odb9.tar.gzttblastnt makeblastdbsconfig.ini.defaults config.inic C€s)|rt}d}n!|r*t}d}n t}d}tdd|g|d|ƒ}|s^dSt||ƒ}|rŸtjj|ƒr›t j |dt ƒnt Stjj |ƒs%t||dƒ}|j d ƒt|d ||||ƒtjj |ƒs%|jd |d |d |ƒdSn|S(Ntbacteriatfungit eukaryotaRsBusco databasest only_cleant ignore_errorss.tar.gzs Downloading BUSCO database...s databasesFailed to download s database from s and unpack it into (tbacteria_db_urlt fungi_db_urlteukaryota_db_urlR tNoneRtostpathtisdirtshutiltrmtreetTruetexistst main_infoRtwarning( tloggert is_prokaryotet is_fungusRturltcladetdirpatht db_dirpathtdownloaded_fpath((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pyt download_db"s0   !c€st|||||d|ƒ‰ˆs)dS|r[tjjˆƒrWtjˆdtƒnˆStˆdƒ}t ‡fd†|Dƒƒ rt ||ƒ rtˆ|dƒ}|j dƒt |||ˆ|ƒt ‡fd†|Dƒƒs|j d|d |d ˆƒdSnˆS( NRRs make.failedc3€s*|] }tjjtˆ|ƒƒVqdS(N(RRR!R(t.0tfpath(t tool_dirpath(sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pys Lss.tar.gzs" Downloading third-party tools...c3€s*|] }tjjtˆ|ƒƒVqdS(N(RRR!R(R-R.(R/(sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pys RssFailed to download s from sand unpack it into (R RRRRRRR RtallRR"RR#(ttoolt tool_versiontrequired_filesR$R'Rtfailed_compilation_flagR+((R/sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pyt download_toolAs" !cC€s^t|dtd|ƒ}t|dtd|ƒ}t|dtdtd|ƒ}|o]|o]|S(NR%RR&(R,R tFalse(R$Rt bacteria_dbt eukaryota_dbtfungi_db((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pytdownload_all_dbXscC€sAtjj|dƒ}tjjtjj|ddƒƒr=|SdS(Ntconfigtcgpslog_reg_parameters_default.cfg(RRRtisfileR(t core_dirpatht expected_path((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pytget_augustus_config_dir_s$cC€s[ddg}xH|D]@}tjj||ƒ}tjjtjj|dƒƒr|SqWdS(Ntscriptstbinsaugustus2browser.pl(RRRR=R(R>texpected_optionstoptR?((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pytget_augustus_scripts_dirfs   !cC€s†d„}tjddtdtdtƒ}|dk rgtjjtjj|ƒƒ}||ƒrg|Sntdtdg|t d|ƒS(NcS€setjj|ddƒ}tjj|ƒ sAtj|tjƒ rEtSt|ƒrat|ƒrat StS(NRBt etraining( RRRR=taccesstX_OKR6R@RER (R)tetraining_path((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pyt*__check_preinstalled_augustus_completenessps )taugustust min_versiontrecommend_versiontmax_allowed_versionRBR( Rtget_path_to_programtaugustus_versiontaugustus_max_allowed_versionRRRRR5t augustus_url(R$RRJtpreinstalled_augustustpreinstalled_augustus_dirpath((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pytdownload_augustusos    c C€sxttttƒƒdƒ}tjr*dnd}i |d6|d6|d6|d6t|ƒd6ttd ƒƒd 6ttd ƒƒd 6t|d ƒd6t|d ƒd6t|ƒd6|d6}t|t ƒ}t|t ƒ} t |ƒ} t | dƒw} xm| D]e} | j ƒj ƒ} | s#qÿn| d}||krJ||| dúss>Failed running BUSCO for all the assemblies. See log files in sE for information (rerun with --debug to keep all intermediate files).isComplete BUSCOst FragmentedtTotals%.2fgY@sFailed running BUSCO for s[. See the log for detailed information (rerun with --debug to keep all intermediate files).sëBUSCO did not fail explicitly but found nothing for all assemblies! Possible reasons and workarounds: 1. Provided assemblies are so small that they do not contain even a single partial BUSCO gene. Not likely but may happen -- nothing to worry then. 2. Incorrect lineage database was used. To run with fungi DB use --fungus, to run with eukaryota DB use --eukaryote, otherwise BUSCO uses bacteria DB. 3. Problem with BUSCO dependencies, most likely Augustus. Check that the binaries in s</bin/ are working properly. If something is wrong with Augustus, you may try to install it yourself (https://github.com/Gaius-Augustus/Augustus or `conda install -c bioconda augustus`) and make sure "augustus" binary is in PATH. Please install the PROPER VERSION of Augustus, we tested BUSCO with augustus-s!, it may also work with augustus-s6, the newer/older versions are not supported. 4. Some other problem with BUSCO. Check the logs (you may need to rerun QUAST with --debug to see all intermediate files). If you cannot solve the problem yourself, post an issue at https://github.com/ablab/quast/issues or write to quast.support@cab.spbu.rusDone.(iii(1tprint_timestamptinfoR RUR6R RR tblast_filenamesRRRR‚tmintlenRt max_threadstmaxR,RdR&RytenvironR‹terrorRtlabel_from_fpath_for_fnameR R}tanyt enumerateRtgetR=RhtintRjt add_fieldtFieldstBUSCO_COMPLETEtfloatt BUSCO_PARTRtcopyR#RPRQtdebugR‘(tcontigs_fpathst output_dirR$tcompilation_successRoRZtn_jobst busco_threadsRnRst contigs_fpathR|tsummary_fpathstzero_output_for_alltitreportt total_buscost part_buscostcomplete_buscostfRv((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pytdoÏs~    $      (     # (+ "  (0t __future__RRtos.pathRRRRtquast_libs.ra_utils.miscRt quast_libsRRRtquast_libs.buscoRtquast_libs.logR tquast_libs.qutilsR R R R RRtLOGGER_DEFAULT_NAMER$RPRQRRRRRR›RfRgR6R,R5R:R@RERURyR}R‹R‘R¼(((sB/home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/run_busco.pyts:  .