STATUS: Parsing control files... -------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: compute-g20-7.deepthought.umd.edu (PID 28015) MPI_COMM_WORLD rank: 0 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- [compute-g20-8:09542] *** Process received signal *** [compute-g20-8:09542] Signal: Segmentation fault (11) [compute-g20-8:09542] Signal code: Address not mapped (1) [compute-g20-8:09542] Failing at address: 0xee00350 [compute-g20-8:09543] *** Process received signal *** [compute-g20-8:09543] Signal: Segmentation fault (11) [compute-g20-8:09543] Signal code: Address not mapped (1) [compute-g20-8:09543] Failing at address: 0xf020c90 [compute-g20-8:09544] *** Process received signal *** [compute-g20-8:09544] Signal: Segmentation fault (11) [compute-g20-8:09544] Signal code: Address not mapped (1) [compute-g20-8:09544] Failing at address: 0x1ad68f10 [compute-g20-8:09545] *** Process received signal *** [compute-g20-8:09545] Signal: Segmentation fault (11) [compute-g20-8:09545] Signal code: Address not mapped (1) [compute-g20-8:09545] Failing at address: 0x84a3188 [compute-g20-8:09545] [ 0] /lib64/libpthread.so.0 [0x2b98fac5eca0] [compute-g20-8:09545] [ 1] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_int_malloc+0x530) [0x2b98f9ea4ec0] [compute-g20-8:09545] [ 2] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_malloc+0x4a) [0x2b98f9ea60ca] [compute-g20-8:09545] [ 3] perl(Perl_safesysmalloc+0x12) [0x481602] [compute-g20-8:09545] [ 4] perl(Perl_savepvn+0x26) [0x4816b6] [compute-g20-8:09545] [ 5] perl(Perl_do_exec3+0x31e) [0x4f715e] [compute-g20-8:09545] [ 6] perl(Perl_my_popen+0x403) [0x484d63] [compute-g20-8:09545] [ 7] perl(Perl_do_openn+0x1696) [0x4f9536] [compute-g20-8:09545] [ 8] perl(Perl_pp_open+0x184) [0x4efc44] [compute-g20-8:09545] [ 9] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09545] [10] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09545] [11] perl(main+0x135) [0x41b485] [compute-g20-8:09545] [12] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b98fae899c4] [compute-g20-8:09545] [13] perl [0x41b299] [compute-g20-8:09545] *** End of error message *** [compute-g20-8:09546] *** Process received signal *** [compute-g20-8:09546] Signal: Segmentation fault (11) [compute-g20-8:09546] Signal code: Address not mapped (1) [compute-g20-8:09546] Failing at address: 0x8240850 [compute-g20-8:09547] *** Process received signal *** [compute-g20-8:09547] Signal: Segmentation fault (11) [compute-g20-8:09547] Signal code: Address not mapped (1) [compute-g20-8:09547] Failing at address: 0xd5c8850 [compute-g20-8:09548] *** Process received signal *** [compute-g20-8:09548] Signal: Segmentation fault (11) [compute-g20-8:09548] Signal code: Address not mapped (1) [compute-g20-8:09548] Failing at address: 0x8c80850 [compute-g20-8:09549] *** Process received signal *** [compute-g20-8:09549] Signal: Segmentation fault (11) [compute-g20-8:09549] Signal code: Address not mapped (1) [compute-g20-8:09549] Failing at address: 0x18d72850 [compute-g20-10:07087] *** Process received signal *** [compute-g20-10:07087] Signal: Segmentation fault (11) [compute-g20-10:07087] Signal code: Address not mapped (1) [compute-g20-10:07087] Failing at address: 0x6659f10 [compute-g20-10:07088] *** Process received signal *** [compute-g20-10:07088] Signal: Segmentation fault (11) [compute-g20-10:07088] Signal code: Address not mapped (1) [compute-g20-10:07088] Failing at address: 0x1fe3b5d0 [compute-g20-10:07089] *** Process received signal *** [compute-g20-10:07089] Signal: Segmentation fault (11) [compute-g20-10:07089] Signal code: Address not mapped (1) [compute-g20-10:07089] Failing at address: 0x9870350 [compute-g20-10:07090] *** Process received signal *** [compute-g20-10:07090] Signal: Segmentation fault (11) [compute-g20-10:07090] Signal code: Address not mapped (1) [compute-g20-10:07090] Failing at address: 0x17bad350 STATUS: Processing and indexing input FASTA files... [compute-g20-8:09567] *** Process received signal *** [compute-g20-8:09567] Signal: Segmentation fault (11) [compute-g20-8:09567] Signal code: Address not mapped (1) [compute-g20-8:09567] Failing at address: 0x1ad5aa10 [compute-g20-8:09567] [ 0] /lib64/libpthread.so.0 [0x2b6de3ce1ca0] [compute-g20-8:09567] [ 1] /lib64/libc.so.6(strlen+0x30) [0x2b6de3f67f40] [compute-g20-8:09567] [ 2] perl(Perl_do_exec3+0x3a) [0x4f6e7a] [compute-g20-8:09567] [ 3] perl(Perl_my_popen+0x403) [0x484d63] [compute-g20-8:09567] [ 4] perl(Perl_do_openn+0x1696) [0x4f9536] [compute-g20-8:09567] [ 5] perl(Perl_pp_open+0x184) [0x4efc44] [compute-g20-8:09567] [ 6] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09567] [ 7] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09567] [ 8] perl(main+0x135) [0x41b485] [compute-g20-8:09567] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b6de3f0c9c4] [compute-g20-8:09567] [10] perl [0x41b299] [compute-g20-8:09567] *** End of error message *** [compute-g20-7:28123] *** Process received signal *** [compute-g20-7:28123] Signal: Segmentation fault (11) [compute-g20-7:28123] Signal code: Address not mapped (1) [compute-g20-7:28123] Failing at address: 0x19ad9f10 STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore To access files for individual sequences use the datastore index: /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_master_datastore_index.log STATUS: Now running MAKER... examining contents of the fasta file and run log [compute-g20-10:07107] *** Process received signal *** [compute-g20-10:07107] Signal: Segmentation fault (11) [compute-g20-10:07107] Signal code: Address not mapped (1) [compute-g20-10:07107] Failing at address: 0x9870362 [compute-g20-10:07107] [ 0] /lib64/libpthread.so.0 [0x2b50c5c8cca0] [compute-g20-10:07107] [ 1] perl [0x487218] [compute-g20-10:07107] [ 2] perl(Perl_hv_common+0xe67) [0x499dd7] [compute-g20-10:07107] [ 3] perl [0x49d9dc] [compute-g20-10:07107] [ 4] perl(Perl_pp_method_named+0x6e) [0x49dd4e] [compute-g20-10:07107] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-10:07107] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-10:07107] [ 7] perl(main+0x135) [0x41b485] [compute-g20-10:07107] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b50c5eb79c4] [compute-g20-10:07107] [ 9] perl [0x41b299] [compute-g20-10:07107] *** End of error message *** examining contents of the fasta file and run log examining contents of the fasta file and run log [compute-g20-10:07108] *** Process received signal *** [compute-g20-10:07108] Signal: Segmentation fault (11) [compute-g20-10:07108] Signal code: Address not mapped (1) [compute-g20-10:07108] Failing at address: 0x1fe3b5c8 examining contents of the fasta file and run log [compute-g20-10:07108] [ 0] /lib64/libpthread.so.0 [0x2b88f6f8dca0] [compute-g20-10:07108] [ 1] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_free+0x22) [0x2b88f61d55b2] [compute-g20-10:07108] [ 2] /lib64/libc.so.6(cfree+0xd1) [0x2b88f7210ad1] [compute-g20-10:07108] [ 3] perl(Perl_sv_setsv_flags+0xb49) [0x4ad919] [compute-g20-10:07108] [ 4] perl(Perl_pp_aassign+0x209) [0x4a3a19] [compute-g20-10:07108] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-10:07108] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-10:07108] [ 7] perl(main+0x135) [0x41b485] [compute-g20-10:07108] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b88f71b89c4] [compute-g20-10:07108] [ 9] perl [0x41b299] [compute-g20-10:07108] *** End of error message *** examining contents of the fasta file and run log [compute-g20-10:07109] *** Process received signal *** [compute-g20-10:07109] Signal: Segmentation fault (11) [compute-g20-10:07109] Signal code: Address not mapped (1) [compute-g20-10:07109] Failing at address: 0x6664ad0 [compute-g20-10:07109] [ 0] /lib64/libpthread.so.0 [0x2b0809664ca0] [compute-g20-10:07109] [ 1] /lib64/libc.so.6 [0x2b08098edada] [compute-g20-10:07109] [ 2] /lib64/libc.so.6(memmove+0x75) [0x2b08098ec095] [compute-g20-10:07109] [ 3] perl(Perl_sv_setpvn+0x7a) [0x4b775a] [compute-g20-10:07109] [ 4] perl(Perl_pp_concat+0xc9) [0x4a5739] [compute-g20-10:07109] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-10:07109] [ 6] perl(Perl_call_sv+0x160) [0x4333a0] [compute-g20-10:07109] [ 7] perl(Perl_magic_methcall+0x182) [0x488c22] [compute-g20-10:07109] [ 8] perl(Perl_magic_setpack+0x52) [0x489292] [compute-g20-10:07109] [ 9] perl(Perl_mg_set+0x66) [0x48aca6] [compute-g20-10:07109] [10] perl(Perl_pp_sassign+0x19c) [0x4a5c8c] [compute-g20-10:07109] [11] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-10:07109] [12] perl(perl_run+0x243) [0x4340f3] [compute-g20-10:07109] [13] perl(main+0x135) [0x41b485] [compute-g20-10:07109] [14] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b080988f9c4] [compute-g20-10:07109] [15] perl [0x41b299] [compute-g20-10:07109] *** End of error message *** 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 --Next Contig-- --Next Contig-- --Next Contig-- examining contents of the fasta file and run log --Next Contig-- Processing run.log file... Processing run.log file... examining contents of the fasta file and run log Processing run.log file... Processing run.log file... --Next Contig-- --Next Contig-- --Next Contig-- --Next Contig-- --Next Contig-- Processing run.log file... Processing run.log file... --Next Contig-- --Next Contig-- Processing run.log file... #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_2 Length: 2857 #--------------------------------------------------------------------- Processing run.log file... MAKER WARNING: The file UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/D5/5A/Gc_UCSC1_contig_17//theVoid.Gc_UCSC1_contig_17/0/Gc_UCSC1_contig_17.0.all.rb.out did not finish on the last run and must be erased Processing run.log file... setting up GFF3 output and fasta chunks Processing run.log file... #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_7 Length: 972 #--------------------------------------------------------------------- [compute-g20-8:09576] *** Process received signal *** [compute-g20-8:09576] Signal: Segmentation fault (11) [compute-g20-8:09576] Signal code: Address not mapped (1) [compute-g20-8:09576] Failing at address: 0x1ad68f08 examining contents of the fasta file and run log #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_3 Length: 2316 #--------------------------------------------------------------------- [compute-g20-8:09576] [ 0] /lib64/libpthread.so.0 [0x2b6de3ce1ca0] [compute-g20-8:09576] [ 1] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_free+0x22) [0x2b6de2f295b2] [compute-g20-8:09576] [ 2] /lib64/libc.so.6(cfree+0xd1) [0x2b6de3f64ad1] [compute-g20-8:09576] [ 3] perl(Perl_sv_setsv_flags+0xb49) [0x4ad919] [compute-g20-8:09576] [ 4] perl(Perl_pp_aassign+0x209) [0x4a3a19] [compute-g20-8:09576] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09576] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09576] [ 7] perl(main+0x135) [0x41b485] [compute-g20-8:09576] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b6de3f0c9c4] [compute-g20-8:09576] [ 9] perl [0x41b299] [compute-g20-8:09576] *** End of error message *** #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_4 Length: 1230 #--------------------------------------------------------------------- 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 [compute-g20-8:09578] *** Process received signal *** [compute-g20-8:09578] Signal: Segmentation fault (11) [compute-g20-8:09578] Signal code: Address not mapped (1) [compute-g20-8:09578] Failing at address: 0xee0af18 [compute-g20-8:09578] [ 0] /lib64/libpthread.so.0 [0x2b03d0637ca0] [compute-g20-8:09578] [ 1] perl(Perl_av_fetch+0x5b) [0x49cf8b] [compute-g20-8:09578] [ 2] perl(Perl_pp_aelem+0x26e) [0x49e48e] [compute-g20-8:09578] [ 3] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09578] [ 4] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09578] [ 5] perl(main+0x135) [0x41b485] [compute-g20-8:09578] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b03d08629c4] [compute-g20-8:09578] [ 7] perl [0x41b299] [compute-g20-8:09578] *** End of error message *** setting up GFF3 output and fasta chunks Processing run.log file... [compute-g20-8:09583] *** Process received signal *** [compute-g20-8:09583] Signal: Segmentation fault (11) [compute-g20-8:09583] Signal code: Address not mapped (1) [compute-g20-8:09583] Failing at address: 0x822b0e2 [compute-g20-8:09582] *** Process received signal *** [compute-g20-8:09582] Signal: Segmentation fault (11) [compute-g20-8:09582] Signal code: Address not mapped (1) [compute-g20-8:09582] Failing at address: 0x8c6b0e2 [compute-g20-8:09583] [ 0] /lib64/libpthread.so.0 [0x2ab7f114dca0] [compute-g20-8:09583] [ 1] perl [0x487218] [compute-g20-8:09583] [ 2] perl(Perl_hv_common+0xe67) [0x499dd7] [compute-g20-8:09583] [ 3] perl [0x49d9dc] [compute-g20-8:09583] [ 4] perl(Perl_pp_method_named+0x6e) [0x49dd4e] [compute-g20-8:09583] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09583] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09583] [ 7] perl(main+0x135) [0x41b485] [compute-g20-8:09583] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2ab7f13789c4] [compute-g20-8:09583] [ 9] perl [0x41b299] [compute-g20-8:09583] *** End of error message *** [compute-g20-8:09582] [ 0] /lib64/libpthread.so.0 [0x2b4eace23ca0] [compute-g20-8:09582] [ 1] perl [0x487218] [compute-g20-8:09582] [ 2] perl(Perl_hv_common+0xe67) [0x499dd7] [compute-g20-8:09582] [ 3] perl [0x49d9dc] [compute-g20-8:09582] [ 4] perl(Perl_pp_method_named+0x6e) [0x49dd4e] [compute-g20-8:09582] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09582] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09582] [ 7] perl(main+0x135) [0x41b485] [compute-g20-8:09582] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b4ead04e9c4] [compute-g20-8:09582] [ 9] perl [0x41b299] [compute-g20-8:09582] *** End of error message *** examining contents of the fasta file and run log [compute-g20-8:09581] *** Process received signal *** [compute-g20-8:09581] Signal: Segmentation fault (11) [compute-g20-8:09581] Signal code: Address not mapped (1) [compute-g20-8:09581] Failing at address: 0x848da08 #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_17 Length: 1413 #--------------------------------------------------------------------- #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_13 Length: 2019 #--------------------------------------------------------------------- [compute-g20-8:09581] [ 0] /lib64/libpthread.so.0 [0x2b98fac5eca0] [compute-g20-8:09581] [ 1] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_free+0x22) [0x2b98f9ea65b2] [compute-g20-8:09581] [ 2] /lib64/libc.so.6(cfree+0xd1) [0x2b98faee1ad1] [compute-g20-8:09581] [ 3] perl(Perl_sv_setsv_flags+0xb49) [0x4ad919] [compute-g20-8:09581] [ 4] perl(Perl_pp_aassign+0x209) [0x4a3a19] [compute-g20-8:09581] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09581] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09581] [ 7] perl(main+0x135) [0x41b485] [compute-g20-8:09581] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b98fae899c4] [compute-g20-8:09581] [ 9] perl [0x41b299] [compute-g20-8:09577] *** Process received signal *** [compute-g20-8:09581] *** End of error message *** [compute-g20-8:09577] Signal: Segmentation fault (11) [compute-g20-8:09577] Signal code: Address not mapped (1) [compute-g20-8:09577] Failing at address: 0xd5b30e2 [compute-g20-8:09577] [ 0] /lib64/libpthread.so.0 [0x2b79d382aca0] [compute-g20-8:09577] [ 1] perl [0x487218] [compute-g20-8:09577] [ 2] perl(Perl_hv_common+0xe67) [0x499dd7] [compute-g20-8:09577] [ 3] perl [0x49d9dc] [compute-g20-8:09577] [ 4] perl(Perl_pp_method_named+0x6e) [0x49dd4e] [compute-g20-8:09577] [ 5] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09577] [ 6] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09577] [ 7] perl(main+0x135) [0x41b485] [compute-g20-8:09577] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b79d3a559c4] [compute-g20-8:09577] [ 9] perl [0x41b299] [compute-g20-8:09577] *** End of error message *** #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_1 Length: 1446 #--------------------------------------------------------------------- setting up GFF3 output and fasta chunks [compute-g20-8:09579] *** Process received signal *** [compute-g20-8:09579] Signal: Segmentation fault (11) [compute-g20-8:09579] Signal code: Address not mapped (1) [compute-g20-8:09579] Failing at address: 0x18d64350 examining contents of the fasta file and run log [compute-g20-8:09579] [ 0] /lib64/libpthread.so.0 [0x2b31b670fca0] [compute-g20-8:09579] [ 1] /usr/local/BerkeleyDB/lib/libdb-4.7.so(__ham_get_meta+0x4c) [0x2b31bbd1bccc] [compute-g20-8:09579] [ 2] /usr/local/BerkeleyDB/lib/libdb-4.7.so [0x2b31bbd103fb] [compute-g20-8:09579] [ 3] /usr/local/BerkeleyDB/lib/libdb-4.7.so(__dbc_get+0x1fa) [0x2b31bbd81f3a] [compute-g20-8:09579] [ 4] /usr/local/BerkeleyDB/lib/libdb-4.7.so(__dbc_get_pp+0xb4) [0x2b31bbd8db04] [compute-g20-8:09579] [ 5] /usr/local/BerkeleyDB/lib/libdb-4.7.so [0x2b31bbce4b85] [compute-g20-8:09579] [ 6] /usr/local/perl/5.16.3-threaded/lib/site_perl/5.16.3/x86_64-linux-thread-multi/auto/DB_File/DB_File.so [0x2b31bbabafc9] [compute-g20-8:09579] [ 7] perl(Perl_pp_entersub+0x58f) [0x49ee4f] [compute-g20-8:09579] [ 8] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-8:09579] [ 9] perl(perl_run+0x243) [0x4340f3] [compute-g20-8:09579] [10] perl(main+0x135) [0x41b485] [compute-g20-8:09579] [11] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b31b693a9c4] [compute-g20-8:09579] [12] perl [0x41b299] [compute-g20-8:09579] *** End of error message *** --Next Contig-- setting up GFF3 output and fasta chunks setting up GFF3 output and fasta chunks --Next Contig-- setting up GFF3 output and fasta chunks --Next Contig-- --Next Contig-- Processing run.log file... MAKER WARNING: The file UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/3B/F3/Gc_UCSC1_contig_26//theVoid.Gc_UCSC1_contig_26/0/Gc_UCSC1_contig_26.0.all.rb.out did not finish on the last run and must be erased --Next Contig-- --Next Contig-- --Next Contig-- #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_18 Length: 937 #--------------------------------------------------------------------- Processing run.log file... Processing run.log file... Processing run.log file... --Next Contig-- FATAL: Thread terminated, causing all processes to fail --> rank=17, hostname=compute-g20-10.deepthought.umd.edu setting up GFF3 output and fasta chunks Processing run.log file... Processing run.log file... #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_14 Length: 6745 #--------------------------------------------------------------------- #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_9 Length: 554 #--------------------------------------------------------------------- MAKER WARNING: The file UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/FB/E4/Gc_UCSC1_contig_22//theVoid.Gc_UCSC1_contig_22/0/Gc_UCSC1_contig_22.0.all.rb.out did not finish on the last run and must be erased setting up GFF3 output and fasta chunks Processing run.log file... setting up GFF3 output and fasta chunks #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_16 Length: 995 #--------------------------------------------------------------------- setting up GFF3 output and fasta chunks #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_26 Length: 1895 #--------------------------------------------------------------------- FATAL: Thread terminated, causing all processes to fail --> rank=16, hostname=compute-g20-10.deepthought.umd.edu #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_23 Length: 618 #--------------------------------------------------------------------- #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_31 Length: 506 #--------------------------------------------------------------------- setting up GFF3 output and fasta chunks setting up GFF3 output and fasta chunks #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_28 Length: 5246 #--------------------------------------------------------------------- MAKER WARNING: The file UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/E5/53/Gc_UCSC1_contig_29//theVoid.Gc_UCSC1_contig_29/0/Gc_UCSC1_contig_29.0.all.rb.out did not finish on the last run and must be erased setting up GFF3 output and fasta chunks setting up GFF3 output and fasta chunks setting up GFF3 output and fasta chunks #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_19 Length: 880 #--------------------------------------------------------------------- #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_22 Length: 831 #--------------------------------------------------------------------- #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_21 Length: 12421 #--------------------------------------------------------------------- doing repeat masking FATAL: Thread terminated, causing all processes to fail --> rank=18, hostname=compute-g20-10.deepthought.umd.edu #--------------------------------------------------------------------- Now starting the contig!! SeqID: Gc_UCSC1_contig_29 Length: 1161 #--------------------------------------------------------------------- doing repeat masking DBD::SQLite::db do failed: disk I/O error at /export/rel50_shadow/glue.umd.edu/software/maker/2.28/.amd64_rel50/bin/../lib/GFFDB.pm line 105. DBD::SQLite::db do failed: disk I/O error at /export/rel50_shadow/glue.umd.edu/software/maker/2.28/.amd64_rel50/bin/../lib/GFFDB.pm line 106. DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /export/rel50_shadow/glue.umd.edu/software/maker/2.28/.amd64_rel50/bin/../lib/GFFDB.pm line 108. DBD::SQLite::db do failed: disk I/O error at /export/rel50_shadow/glue.umd.edu/software/maker/2.28/.amd64_rel50/bin/../lib/GFFDB.pm line 110. [compute-g20-7.deepthought.umd.edu:28014] 19 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork [compute-g20-7.deepthought.umd.edu:28014] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/0F/67/Gc_UCSC1_contig_9//theVoid.Gc_UCSC1_contig_9/0/Gc_UCSC1_contig_9.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/0F/67/Gc_UCSC1_contig_9//theVoid.Gc_UCSC1_contig_9/0 -pa 1 #-------------------------------# SIGTERM received doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/D5/5A/Gc_UCSC1_contig_17//theVoid.Gc_UCSC1_contig_17/0/Gc_UCSC1_contig_17.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/D5/5A/Gc_UCSC1_contig_17//theVoid.Gc_UCSC1_contig_17/0 -pa 1 #-------------------------------# SIGTERM received SIGTERM received [compute-g20-7:28161] *** Process received signal *** [compute-g20-7:28161] Signal: Segmentation fault (11) [compute-g20-7:28161] Signal code: Address not mapped (1) [compute-g20-7:28161] Failing at address: 0x19a33ad0 [compute-g20-7:28161] [ 0] /lib64/libpthread.so.0 [0x2b9e1cd6bca0] [compute-g20-7:28161] [ 1] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_int_malloc+0xb0) [0x2b9e1bfb1a40] [compute-g20-7:28161] [ 2] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_memory_ptmalloc2_malloc+0x4a) [0x2b9e1bfb30ca] [compute-g20-7:28161] [ 3] perl(Perl_safesysmalloc+0x12) [0x481602] [compute-g20-7:28161] [ 4] perl(Perl_do_exec3+0x46) [0x4f6e86] [compute-g20-7:28161] [ 5] perl(Perl_my_popen+0x403) [0x484d63] [compute-g20-7:28161] [ 6] perl(Perl_pp_backtick+0xc2) [0x4f0752] [compute-g20-7:28161] [ 7] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-7:28161] [ 8] perl(Perl_call_sv+0x4d1) [0x433711] [compute-g20-7:28161] [ 9] perl(Perl_sighandler+0x208) [0x4876c8] [compute-g20-7:28161] [10] /lib64/libpthread.so.0 [0x2b9e1cd6bca0] [compute-g20-7:28161] [11] /usr/local/ofed/1.5.4/lib64/libmthca-rdmav2.so [0x2b9e29187bbc] [compute-g20-7:28161] [12] /cell_root/software/openmpi/1.6/gnu/sys/lib/openmpi/mca_btl_openib.so [0x2b9e2686a8dd] [compute-g20-7:28161] [13] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(opal_progress+0x5b) [0x2b9e1bfc93cb] [compute-g20-7:28161] [14] /cell_root/software/openmpi/1.6/gnu/sys/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_recv+0x205) [0x2b9e25e22005] [compute-g20-7:28161] [15] /cell_root/software/openmpi/1.6/gnu/sys/lib/libmpi.so(PMPI_Recv+0x14f) [0x2b9e1bf2927f] [compute-g20-7:28161] [16] /export/rel50_shadow/glue.umd.edu/software/maker/2.28/.amd64_rel50/perl/lib/auto/Parallel/Application/MPI/MPI.so(_MPI_Recv+0x59) [0x2b9e23ba8d69] [compute-g20-7:28161] [17] /export/rel50_shadow/glue.umd.edu/software/maker/2.28/.amd64_rel50/perl/lib/auto/Parallel/Application/MPI/MPI.so [0x2b9e23ba8f58] [compute-g20-7:28161] [18] perl(Perl_pp_entersub+0x58f) [0x49ee4f] [compute-g20-7:28161] [19] perl(Perl_runops_standard+0xe) [0x49d5ce] [compute-g20-7:28161] [20] perl(perl_run+0x243) [0x4340f3] [compute-g20-7:28161] [21] perl(main+0x135) [0x41b485] [compute-g20-7:28161] [22] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b9e1cf969c4] [compute-g20-7:28161] [23] perl [0x41b299] [compute-g20-7:28161] *** End of error message *** running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/DC/D5/Gc_UCSC1_contig_18//theVoid.Gc_UCSC1_contig_18/0/Gc_UCSC1_contig_18.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/DC/D5/Gc_UCSC1_contig_18//theVoid.Gc_UCSC1_contig_18/0 -pa 1 #-------------------------------# SIGTERM received doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/BE/77/Gc_UCSC1_contig_16//theVoid.Gc_UCSC1_contig_16/0/Gc_UCSC1_contig_16.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/BE/77/Gc_UCSC1_contig_16//theVoid.Gc_UCSC1_contig_16/0 -pa 1 #-------------------------------# SIGTERM received doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/1C/8A/Gc_UCSC1_contig_14//theVoid.Gc_UCSC1_contig_14/0/Gc_UCSC1_contig_14.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/1C/8A/Gc_UCSC1_contig_14//theVoid.Gc_UCSC1_contig_14/0 -pa 1 #-------------------------------# SIGTERM received doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/CB/E5/Gc_UCSC1_contig_13//theVoid.Gc_UCSC1_contig_13/0/Gc_UCSC1_contig_13.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/CB/E5/Gc_UCSC1_contig_13//theVoid.Gc_UCSC1_contig_13/0 -pa 1 #-------------------------------# SIGTERM received Perl exited with active threads: 1 running and unjoined 0 finished and unjoined 0 running and detached doing repeat masking running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_amJ13c; /a/g20-fs1/software/dt-sw0/RepeatMasker/4.0.3/RepeatMasker /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/AA/A6/Gc_UCSC1_contig_1//theVoid.Gc_UCSC1_contig_1/0/Gc_UCSC1_contig_1.0.all.rb -species all -dir /export/lustre_1/imisner/Maker/UCSC1_CLC_de_novo.maker.output/UCSC1_CLC_de_novo_datastore/AA/A6/Gc_UCSC1_contig_1//theVoid.Gc_UCSC1_contig_1/0 -pa 1 #-------------------------------# SIGTERM received -------------------------------------------------------------------------- mpirun has exited due to process rank 17 with PID 7052 on node compute-g20-10.deepthought.umd.edu exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- SIGTERM received SIGTERM received Perl exited with active threads: 0 running and unjoined 1 finished and unjoined 0 running and detached FATAL: Thread terminated, causing all processes to fail --> rank=14, hostname=compute-g20-8.deepthought.umd.edu Perl exited with active threads: 0 running and unjoined 1 finished and unjoined 0 running and detached FATAL: Thread terminated, causing all processes to fail --> rank=12, hostname=compute-g20-8.deepthought.umd.edu [compute-g20-8:09470] *** Process received signal *** [compute-g20-8:09470] Signal: Segmentation fault (11) [compute-g20-8:09470] Signal code: Address not mapped (1) [compute-g20-8:09470] Failing at address: 0x4b0 [compute-g20-8:09470] [ 0] /lib64/libpthread.so.0 [0x2b03d0637ca0] [compute-g20-8:09470] [ 1] perl(Perl_csighandler+0x23) [0x488103] [compute-g20-8:09470] [ 2] /lib64/libpthread.so.0 [0x2b03d0637ca0] [compute-g20-8:09470] [ 3] /lib64/libc.so.6(__select+0x62) [0x2b03d0913402] [compute-g20-8:09470] [ 4] /cell_root/software/openmpi/1.6/gnu/sys/lib/openmpi/mca_btl_openib.so [0x2b03da142ff3] [compute-g20-8:09470] [ 5] /lib64/libpthread.so.0 [0x2b03d062f83d] [compute-g20-8:09470] [ 6] /lib64/libc.so.6(clone+0x6d) [0x2b03d091a26d] [compute-g20-8:09470] *** End of error message *** Perl exited with active threads: 0 running and unjoined 1 finished and unjoined 0 running and detached FATAL: Thread terminated, causing all processes to fail --> rank=11, hostname=compute-g20-8.deepthought.umd.edu setting up GFF3 output and fasta chunks FATAL: Thread terminated, causing all processes to fail --> rank=10, hostname=compute-g20-8.deepthought.umd.edu setting up GFF3 output and fasta chunks FATAL: Thread terminated, causing all processes to fail --> rank=13, hostname=compute-g20-8.deepthought.umd.edu FATAL: Thread terminated, causing all processes to fail --> rank=15, hostname=compute-g20-8.deepthought.umd.edu