Question: Error galaxy: repeat explorer local
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gravatar for efeso911
10 months ago by
efeso9110
efeso9110 wrote:

Error while running paired reads:

/home/galaxy-dist/tools/umbr_programs/seqclust/programs/seqClust.sh: línea 555: 14954 Terminado (killed) $PROG_COMMUNITY/convert -i hitsort_PID90_LCOV55_Int -o hitsort_PID90_LCOV55_Int.bin -w weights

pipeline version: failed to get version number! This is clustering pipeline

GRAPH BASED CLUSTERING


Data preparation started: 2017-02-14 19:01

PRE-RUN ANALYSIS 2017-02-14 19:01


copying sequence files saved file no. 0 (3000 sequences, 300000 bp) saved file no. 1 (3000 sequences, 299975 bp) saved file no. 2 (3000 sequences, 299982 bp) saved file no. 3 (3000 sequences, 299956 bp) saved file no. 4 (3000 sequences, 300000 bp) saved file no. 5 (3000 sequences, 299952 bp) saved file no. 6 (2000 sequences, 200000 bp) Done, total sequences saved: 20000 (1999865 bp) analyzing all-to-all similarities The graph with 20,000 nodes has 354796 edges Number of sequences total: 1000000 estimated maximal number of nodes: 992536

Copying (and sampling if neccessary) raw data... 2017-02-14 19:02 sequences names changed Number of sequences: 992536, total length: 99243508, avrg. length: 100.0


SYSTEM SETTINGS: input parameters: WD=/home/galaxy-dist/tools/umbr_programs/seqclust/programs DATA=/home/galaxy-dist/database/files/000/dataset_421.dat STARTDIR=/home/galaxy-dist/database/job_working_directory/000/174 PROC=8 OVL=40 CAPARGS='-o 40 -p 80' MINCL=99 BLASTGR=1000 MINRD=5 CODE=seqClust CONFIGFILE=/home/galaxy-dist/tools/umbr_programs/seqclust/programs/seqclust.config BASEDIR=/home/galaxy-dist/database/job_working_directory/000/174/seqClust PAIREDREADS=false MGBLAST_OVERLAP=55

CONFIGFILE content: export TGICL=$GALAXY_DIR/tools//umbr_utils/tgicl_linux # set according your local installation export PROG_COMMUNITY=$GALAXY_DIR/tools/umbr_utils/louvain # set according your local installation export OGDF=$GALAXY_DIR/tools/umbr_utils/OGDF/runOGDFlayout export DOMAINDATABASE=$GALAXY_DIR/tool-data/domains/TE_domains_newest.fasta # DO NOT MODIFY! export DOMAIN_TYPES=$GALAXY_DIR/tool-data/domains/classification_newest.csv # DO NOT MODIFY! export DATABASE_PBS=$GALAXY_DIR/tool-data/tRNA/tRNAs_arabidopsis_unique # DO NOT MODIFY! export DNADATABASE=$GALAXY_DIR/tool-data/dna_database/dna_database.fasta # DO NOT MODIFY export REPEAT_MASKER=$GALAXY_DIR/RepeatMasker # set according your local installation export RPSBLAST_DATABASE=$GALAXY_DIR/rps-blast/Cdd # set according your local installation export RPSBLAST_DATABASE_ANNOTATION=$GALAXY_DIR/rps-blast/cddid_all.tbl # set according your local installation export JSLIB=$GALAXY_DIR/tools/umbr_programs/interactive_graph/js # DO NOT MODIFY export MIN_MINCL=20 #limit for minimal size of the MINCL, DO NOT MODIFY export MAXEDGES=350000000 # depends on computer memory determine maximal amount of data which could be process

recomendations 16G RAM then MAXEDGES~341576829

export MAXEDGES_FOR_LAYOUT=25000000 # adjusted down for fmmm layout export MAXNODES_FOR_LAYOUT=50000 export PROC_LAYOUT=4

by default maximum memory and cpu is used

To limit cpu and memory usage, uncomment and modify following lines to set PROC and MAX_MEM variables

export PROC=8

export MAX_MEM=4060912 # in kB

TGICL=/home/galaxy-dist/tools//umbr_utils/tgicl_linux PROG_COMMUNITY=/home/galaxy-dist/tools/umbr_utils/louvain DOMAINDATABASE=/home/galaxy-dist/tool-data/domains/TE_domains_newest.fasta DOMAIN_TYPES=/home/galaxy-dist/tool-data/domains/classification_newest.csv REPEAT_MASKER=/home/galaxy-dist/RepeatMasker



Runnig mgblast. 2017-02-14 19:03 PROC was set to 8 for mgblast BASEDIR=/home/galaxy-dist/database/job_working_directory/000/174/seqClust CAPARGS='-o 40 -p 80' CODE=seqClust COLORTERM=xfce4-terminal CONFIGFILE=/home/galaxy-dist/tools/umbr_programs/seqclust/programs/seqclust.config CUSTOM_RM_DATABASE= DATABASE_PBS=/home/galaxy-dist/tool-data/tRNA/tRNAs_arabidopsis_unique DATA=/home/galaxy-dist/database/files/000/dataset_421.dat DISPLAY=:50.0 DNADATABASE=/home/galaxy-dist/tool-data/dna_database/dna_database.fasta DOMAINDATABASE=/home/galaxy-dist/tool-data/domains/TE_domains_newest.fasta DOMAIN_TYPES=/home/galaxy-dist/tool-data/domains/classification_newest.csv GALAXY_CONFIG_FILE=config/galaxy.ini GALAXY_DIR=/home/galaxy-dist GALAXY_SLOTS=1 HOME=/home/alex HTMLEXTRA=/home/galaxy-dist/database/job_working_directory/000/174/dataset_425_files HTMLFILE=/home/galaxy-dist/database/files/000/dataset_425.dat JSLIB=/home/galaxy-dist/tools/umbr_programs/interactive_graph/js LANG=es_ES.UTF-8 LOGFILE=logfile.txt LOGNAME=root LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36: MAIL=/var/mail/root MAXEDGES=350000000 MAXEDGES_FOR_LAYOUT=25000000 MAX_MEM=20560148 MAXNODES_FOR_LAYOUT=50000 MGBLAST_OVERLAP=55 MINCL=99 MINCL_PERC=0.01 MIN_MINCL=20 NSEQ_INPUT=992536 OGDF=/home/galaxy-dist/tools/umbr_utils/OGDF/runOGDFlayout OLDPWD=/home/galaxy-dist/database/job_working_directory/000/174/seqClust OVL=40 PAIREDREADS=false PATH=/home/galaxy-dist/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin PERL_HASH_SEED=0 PERL_PERTURB_KEYS=0 PREFIX_LENGTH=0 PROC=8 PROC_LAYOUT=4 PROG_COMMUNITY=/home/galaxy-dist/tools/umbr_utils/louvain PROG=/home/galaxy-dist/tools/umbr_programs/seqclust/programs PWD=/home/galaxy-dist/database/job_working_directory/000/174/seqClust/sequences PYTHONPATH=/home/galaxy-dist/lib QT_GRAPHICSSYSTEM=native RECLUSTERING=false REPEAT_MASKER=/home/galaxy-dist/RepeatMasker RM_DATABASE=None RPSBLAST_DATABASE_ANNOTATION=/home/galaxy-dist/rps-blast/cddid_all.tbl RPSBLAST_DATABASE=/home/galaxy-dist/rps-blast/Cdd SEQ2EXTRACT= SEQ2EXTRACT_KEEP=10 SHELL=/bin/bash SHLVL=2 SQ_RENAME=True STARTDIR=/home/galaxy-dist/database/job_working_directory/000/174 SUDO_COMMAND=/bin/sh ./run.sh SUDO_GID=1002 SUDO_UID=1002 SUDO_USER=alex TEMP=/home/galaxy-dist/database/tmp TERM=xterm TGICL=/home/galaxy-dist/tools//umbr_utils/tgicl_linux USERNAME=root USER=root _=/usr/bin/env VIRTUAL_ENV=/home/galaxy-dist/.venv XAUTHORITY=/home/alex/.Xauthority ZIPCLUST=False 992536 entries from file seqClust were indexed in file seqClust.cidx 2017-02-14 19:03 {'mgblast_output_dir': '/home/galaxy-dist/database/job_working_directory/000/174/seqClust/mgblast', 'hitsort_file': '/home/galaxy-dist/database/job_working_directory/000/174/seqClust/clustering/hitsort_PID90_LCOV55', 'sequences': '/home/galaxy-dist/database/job_working_directory/000/174/seqClust/sequences/seqClust', 'min_overlap': '55', 'mgblastdir': '/home/galaxy-dist/tools//umbr_utils/tgicl_linux/bin/'} 55

done 2017-02-14 23:23 Running blastx agaist database of protein domains 2017-02-14 23:23


Running blastn agaist database of rDNA/plastid/mitochiondial sequences 2017-02-14 23:43


10 Clustering step 1 - renaming read names using integers 2017-02-14 23:56 Converting hitsort to binary format 2017-02-15 00:20

software error • 345 views
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