nohup: ignoring input -------------------------------------------------------------------------- WARNING: Failed to open "OpenIB-cma" [DAT_PROVIDER_NOT_FOUND:DAT_NAME_NOT_REGISTERED]. This may be a real error or it may be an invalid entry in the uDAPL Registry which is contained in the dat.conf file. Contact your local System Administrator to confirm the availability of the interfaces in the dat.conf file. STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... [xxx.pt:05245] 407 more processes have sent help message help-mpi-btl-udapl.txt / dat_ia_open fail [xxx.pt:05245] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [xxx.pt:05245] 50 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore To access files for individual sequences use the datastore index: ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_master_datastore_index.log STATUS: Now running MAKER... examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log examining contents of the fasta file and run log "All it's run ok until here" Thread 1 terminated abnormally: ../dna.maker.output/mpi_blastdb/dna%2Efa.mpi.1/dna%2Efa.mpi.1.0 --> rank=8, hostname=compute-0-1.local, at ../Analysis/Geno/maker/bin/maker line 1451 thread 1. --> rank=8, hostname=compute-0-1.local deleted:0 hits deleted:0 hits preparing ab-inits deleted:0 hits deleted:0 hits FATAL: Thread terminated, causing all processes to fail --> rank=8, hostname=compute-0-1.local deleted:0 hits #--------------------------------------------------------------------- Now starting the contig!! SeqID: scaffold7028 Length: 23929 #--------------------------------------------------------------------- doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_zWjQ8S/rna%2Efa.mpi.10.0 -query /tmp/maker_zWjQ8S/33/scaffold7015.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/A4/0D/scaffold7015//theVoid.scaffold7015/0/scaffold7015.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.0.blastn #-------------------------------# setting up GFF3 output and fasta chunks running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CO49169%7CEF1A_MANES.for.3294-8880.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.3294-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3294-8880.sp%7CO49169%7CEF1A_MANES.p.exonerate #-------------------------------# deleted:0 hits doing blastx of proteins gathering ab-init output files doing blastx of proteins running blast search. #--------- command -------------# Widget::blastx: ../anaconda3/bin/blastx -db /tmp/maker_zfVjEK/prot%2Efa.mpi.10.1 -query /tmp/maker_zfVjEK/22/scaffold7002.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/3C/2E/scaffold7002//theVoid.scaffold7002/0/scaffold7002.0.prot%2Efa.blastx.temp_dir/prot%2Efa.mpi.10.1.blastx #-------------------------------# running blast search. #--------- command -------------# Widget::blastx: ../anaconda3/bin/blastx -db /tmp/maker_ltQDJ_/prot%2Efa.mpi.10.8 -query /tmp/maker_ltQDJ_/29/scaffold6968.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/54/76/scaffold6968//theVoid.scaffold6968/0/scaffold6968.0.prot%2Efa.blastx.temp_dir/prot%2Efa.mpi.10.8.blastx #-------------------------------# doing blastx repeats running blast search. #--------- command -------------# Widget::blastx: ../anaconda3/bin/blastx -db /tmp/maker_zWjQ8S/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_zWjQ8S/42/scaffold7012.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/A6/65/scaffold7012//theVoid.scaffold7012/0/scaffold7012.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner #-------------------------------# doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_zfVjEK/rna%2Efa.mpi.10.8 -query /tmp/maker_zfVjEK/21/scaffold7007.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/7B/87/scaffold7007//theVoid.scaffold7007/0/scaffold7007.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.8.blastn #-------------------------------# doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_zWjQ8S/rna%2Efa.mpi.10.1 -query /tmp/maker_zWjQ8S/33/scaffold7015.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/A4/0D/scaffold7015//theVoid.scaffold7015/0/scaffold7015.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.1.blastn #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CP17508%7CEF1A3_XENLA.for.3285-8880.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.3285-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3285-8880.sp%7CP17508%7CEF1A3_XENLA.p.exonerate #-------------------------------# doing blastx repeats running blast search. #--------- command -------------# Widget::blastx: ../anaconda3/bin/blastx -db /tmp/maker_zWjQ8S/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_zWjQ8S/43/scaffold7013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/9C/8D/scaffold7013//theVoid.scaffold7013/0/scaffold7013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner #-------------------------------# doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_Ayb5sE; ../anaconda3/share/RepeatMasker/RepeatMasker ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/E5/19/scaffold7028//theVoid.scaffold7028/0/scaffold7028.0.all.rb -species all -dir ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/E5/19/scaffold7028//theVoid.scaffold7028/0 -pa 1 #-------------------------------# deleted:0 hits deleted:0 hits deleted:0 hits deleted:0 hits doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_zWjQ8S/rna%2Efa.mpi.10.2 -query /tmp/maker_zWjQ8S/33/scaffold7015.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/A4/0D/scaffold7015//theVoid.scaffold7015/0/scaffold7015.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.2.blastn #-------------------------------# doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_k8gTks/rna%2Efa.mpi.10.0 -query /tmp/maker_k8gTks/10/scaffold7008.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/8C/09/scaffold7008//theVoid.scaffold7008/0/scaffold7008.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.0.blastn #-------------------------------# doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_zfVjEK/rna%2Efa.mpi.10.9 -query /tmp/maker_zfVjEK/21/scaffold7007.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/7B/87/scaffold7007//theVoid.scaffold7007/0/scaffold7007.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.9.blastn #-------------------------------# deleted:0 hits [xxx.pt][[28096,1],35][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached deleted:0 hits [xxx.pt][[28096,1],43][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],44][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],46][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received deleted:0 hits [xxx.pt][[28096,1],41][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_zWjQ8S; ../anaconda3/share/RepeatMasker/RepeatMasker ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/18/23/scaffold7029//theVoid.scaffold7029/0/scaffold7029.0.EX_lib%2Efa.specific -dir ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/18/23/scaffold7029//theVoid.scaffold7029/0 -pa 1 -lib ../Analysis/Geno/EX_Annotation/Soap_23/EX_lib.fa #-------------------------------# SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],40][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:32 hits SIGTERM received [xxx.pt][[28096,1],50][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:0 hits SIGTERM received [xxx.pt][[28096,1],49][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/49/sp%7CQ9BQI4%7CCCDC3_HUMAN.for.6196-12253.49.fasta -t /tmp/maker_zWjQ8S/49/scaffold6941.6196-12253.49.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/49/scaffold6941.6196-12253.sp%7CQ9BQI4%7CCCDC3_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/49/sp%7CQ9D6Y1%7CCCDC3_MOUSE.for.6199-12253.49.fasta -t /tmp/maker_zWjQ8S/49/scaffold6941.6199-12253.49.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/49/scaffold6941.6199-12253.sp%7CQ9D6Y1%7CCCDC3_MOUSE.p.exonerate #-------------------------------# cleaning blastx... SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],38][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],36][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:1 hits SIGTERM received [xxx.pt][[28096,1],42][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:0 hits SIGTERM received [xxx.pt][[28096,1],48][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received doing blastx repeats running blast search. #--------- command -------------# Widget::blastx: ../anaconda3/bin/blastx -db /tmp/maker_zWjQ8S/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_zWjQ8S/45/scaffold7010.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/54/EF/scaffold7010//theVoid.scaffold7010/0/scaffold7010.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner #-------------------------------# [xxx.pt][[28096,1],45][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:0 hits SIGTERM received [xxx.pt][[28096,1],34][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],47][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ13634%7CCAD18_HUMAN.for.1240-18588.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1240-18588.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1240-18588.sp%7CQ13634%7CCAD18_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP70407%7CCADH9_MOUSE.for.1240-18624.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1240-18624.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1240-18624.sp%7CP70407%7CCADH9_MOUSE.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ63315%7CCAD22_RAT.for.1237-18600.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1237-18600.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1237-18600.sp%7CQ63315%7CCAD22_RAT.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP55289%7CCAD12_HUMAN.for.1240-16680.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1240-16680.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1240-16680.sp%7CP55289%7CCAD12_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP55286%7CCADH8_HUMAN.for.1216-18615.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1216-18615.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1216-18615.sp%7CP55286%7CCADH8_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ6PFX6%7CCAD24_MOUSE.for.1216-16680.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1216-16680.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1216-16680.sp%7CQ6PFX6%7CCAD24_MOUSE.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ9Y6N8%7CCAD10_HUMAN.for.1240-18612.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.1240-18612.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.1240-18612.sp%7CQ9Y6N8%7CCAD10_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ13634%7CCAD18_HUMAN.for.28919-39320.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39320.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39320.sp%7CQ13634%7CCAD18_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ8BM92%7CCADH7_MOUS[xxx.pt][[28096,1],39][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [xxx.pt][[28096,1],37][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:0 hits SIGTERM received SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached E.for.28919-39311.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.sp%7CQ8BM92%7CCADH7_MOUSE.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ3SWX5%7CCADH6_BOVIN.for.28919-39323.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39323.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39323.sp%7CQ3SWX5%7CCADH6_BOVIN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ5DWV2%7CCADH7_RAT.for.28919-39311.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.sp%7CQ5DWV2%7CCADH7_RAT.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ8QGH3%7CCAD20_CHICK.for.28919-39326.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39326.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39326.sp%7CQ8QGH3%7CCAD20_CHICK.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ8AYD0%7CCADH5_CHICK.for.28916-39311.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28916-39311.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28916-39311.sp%7CQ8AYD0%7CCADH5_CHICK.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP33151%7CCADH5_HUMAN.for.28919-39311.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.sp%7CP33151%7CCADH5_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ90763%7CCADH7_CHICK.for.28919-39311.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.28919-39311.sp%7CQ90763%7CCADH7_CHICK.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP70408%7CCAD10_MOUSE.for.58035-68454.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.58035-68454.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.58035-68454.sp%7CP70408%7CCAD10_MOUSE.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CO93319%7CCAD11_CHICK.for.58122-68454.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.58122-68454.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.58122-68454.sp%7CO93319%7CCAD11_CHICK.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP55287%7CCAD11_HUMAN.for.58122-68454.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.58122-68454.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.58122-68454.sp%7CP55287%7CCAD11_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ5DWV2%7CCADH7_RAT.for.58140-68454.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.58140-68454.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.58140-68454.sp%7CQ5DWV2%7CCADH7_RAT.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ8QGH3%7CCAD20_CHICK.for.58122-68678.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.58122-68678.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.58122-68678.sp%7CQ8QGH3%7CCAD20_CHICK.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ8AYD0%7CCADH5_CHICK.for.59925-68529.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.59925-68529.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.59925-68529.sp%7CQ8AYD0%7CCADH5_CHICK.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CP33151%7CCADH5_HUMAN.for.59925-68415.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.59925-68415.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.59925-68415.sp%7CP33151%7CCADH5_HUMAN.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_zWjQ8S/47/sp%7CQ90763%7CCADH7_CHICK.for.58155-68454.47.fasta -t /tmp/maker_zWjQ8S/47/scaffold6863.58155-68454.47.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_zWjQ8S/47/scaffold6863.58155-68454.sp%7CQ90763%7CCADH7_CHICK.p.exonerate #-------------------------------# cleaning blastx... in cluster::shadow_cluster... ...finished clustering. cleaning clusters.... total clusters:1 now processing 0 ...processing 0 of 6 ...processing 1 of 6 ...processing 2 of 6 ...processing 3 of 6 ...processing 4 of 6 ...processing 5 of 6 in cluster::shadow_cluster... ...finished clustering. cleaning clusters.... total clusters:1 now processing 0 ...processing 0 of 5 ...processing 1 of 5 ...processing 2 of 5 ...processing 3 of 5 ...processing 4 of 5 SIGTERM received [compute-0-3.local][[28096,1],19][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-2.local][[28096,1],14][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-6.local][[28096,1],30][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached SIGTERM received deleted:0 hits [compute-0-1.local][[28096,1],9][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received deleted:0 hits Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_s1CLvz; ../anaconda3/share/RepeatMasker/RepeatMasker ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/EA/98/scaffold7023//theVoid.scaffold7023/0/scaffold7023.0.EX_lib%2Efa.specific -dir ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/EA/98/scaffold7023//theVoid.scaffold7023/0 -pa 1 -lib ../Analysis/Geno/EX_Annotation/Soap_23/EX_lib.fa #-------------------------------# SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-3.local][[28096,1],20][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CO64937%7CEF1A_ORYSJ.for.4279-8880.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.4279-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.4279-8880.sp%7CO64937%7CEF1A_ORYSJ.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CQ5R1X2%7CEF1A1_PANTR.for.3279-8880.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.3279-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3279-8880.sp%7CQ5R1X2%7CEF1A1_PANTR.p.exonerate #-------------------------------# [compute-0-2.local][[28096,1],13][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CQ8GTY0%7CEF1A4_ARATH.for.3294-8880.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.3294-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3294-8880.sp%7CQ8GTY0%7CEF1A4_ARATH.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CA0RUM4%7CEF1A_CENSY.for.4252-6091.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.4252-6091.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.4252-6091.sp%7CA0RUM4%7CEF1A_CENSY.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CQ2HJN9%7CEF1A4_OSCTI.for.3294-8877.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.3294-8877.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3294-8877.sp%7CQ2HJN9%7CEF1A4_OSCTI.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CP07810%7CEF1A_METVA.for.4279-6091.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.4279-6091.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.4279-6091.sp%7CP07810%7CEF1A_METVA.p.exonerate #-------------------------------# SIGTERM received running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CP41752%7CEF1A_ASHGO.for.3285-8880.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.3285-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3285-8880.sp%7CP41752%7CEF1A_ASHGO.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CA7I656%7CEF1A_METB6.for.4279-6091.13.fasta -t /tmp/maker_Ayb5sE/13/scaffold6931.4279-6091.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.4279-6091.sp%7CA7I656%7CEF1A_METB6.p.exonerate #-------------------------------# running exonerate search. #--------- command -------------# Widget::exonerate::protein2genome: ../anaconda3/bin/exonerate -q /tmp/maker_Ayb5sE/13/sp%7CP17507%7CEF1A2_XENLA.for.3285-8880.13.fa[compute-0-6.local][[28096,1],32][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_ltQDJ_; ../anaconda3/share/RepeatMasker/RepeatMasker ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/09/3D/scaffold7019//theVoid.scaffold7019/0/scaffold7019.0.EX_lib%2Efa.specific -dir ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/09/3D/scaffold7019//theVoid.scaffold7019/0 -pa 1 -lib ../Analysis/Geno/EX_Annotation/Soap_23/EX_lib.fa #-------------------------------# SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-3.local][[28096,1],23][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-6.local][[28096,1],28][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-1.local][[28096,1],11][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-3.local][[28096,1],22][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received deleted:0 hits Perl exited with active threads: 0 running and unjoined 1 finished and unjoined 0 running and detached collecting blastx reports [compute-0-2.local][[28096,1],15][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached deleted:0 hits doing blastn of ESTs running blast search. #--------- command -------------# Widget::blastn: ../anaconda3/bin/blastn -db /tmp/maker_k8gTks/rna%2Efa.mpi.10.1 -query /tmp/maker_k8gTks/10/scaffold7008.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out ../Analysis/Geno/EX_Annotation/Soap_23/dna.maker.output/dna_datastore/8C/09/scaffold7008//theVoid.scaffold7008/0/scaffold7008.0.rna%2Efa.blastn.temp_dir/rna%2Efa.mpi.10.1.blastn #-------------------------------# deleted:0 hits [compute-0-1.local][[28096,1],10][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received SIGTERM received SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-2.local][[28096,1],16][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) deleted:1 hits SIGTERM received Perl exited with active threads: 0 running and unjoined 1 finished and unjoined 0 running and detached [compute-0-6.local][[28096,1],31][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached deleted:1 hits [compute-0-1.local][[28096,1],7][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached deleted:0 hits [compute-0-3.local][[28096,1],21][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received [compute-0-2.local][[28096,1],17][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached [compute-0-6.local][[28096,1],29][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached sta -t /tmp/maker_Ayb5sE/13/scaffold6931.3285-8880.13.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_Ayb5sE/13/scaffold6931.3285-8880.sp%7CP17507%7CEF1A2_XENLA.p.exonerate #-------------------------------# Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached