directories

(base) [04:32 asharifi@oak: ~/mostafa/Applications/abyss]$ cd
(base) [04:33 asharifi@oak: ~]$ cd usr/bin/
(base) [04:33 asharifi@oak: ~/usr/bin]$ ls
bin      lib           ortecc      orted     orte-info  orterun      orte-submit  oshcc    oshmem_info  share    shmemfort  skype
include  opal_wrapper  orte-clean  orte-dvm  orte-ps    orte-server  orte-top     oshfort  oshrun       shmemcc  shmemrun
(base) [04:33 asharifi@oak: ~/usr/bin]$ cd bin/
(base) [04:33 asharifi@oak: ~/usr/bin/bin]$ ls
ABYSS                abyss-bowtie2  abyss-dida         abyss-gapfill   abyss-longseqdist  abyss-pe          abyss-todot    DistanceEst-ssq  Overlap
abyss-align          abyss-bwa      abyss-fac          abyss-gc        abyss-map          abyss-samtoafg    abyss-tofastq  KAligner         ParseAligns
abyss-bloom          abyss-bwamem   abyss-fatoagp      abyss-index     abyss-map-ssq      abyss-samtobreak  AdjList        konnector        PathConsensus
abyss-bloom-dbg      abyss-bwasw    abyss-filtergraph  abyss-junction  abyss-mergepairs   abyss-scaffold    Consensus      logcounter       PathOverlap
abyss-bloom-dist.mk  abyss-db-csv   abyss-fixmate      abyss-kaligner  abyss-overlap      abyss-sealer      DAssembler     MergeContigs     PopBubbles
abyss-bowtie         abyss-db-txt   abyss-fixmate-ssq  abyss-layout    abyss-paired-dbg   abyss-tabtomd     DistanceEst    MergePaths       SimpleGraph
(base) [04:33 asharifi@oak: ~/usr/bin/bin]$ abyss-pe versions
abyss-pe (ABySS) 2.1.4
Written by Shaun Jackman and Anthony Raymond.
Copyright 2012 Canada's Michael Smith Genome Science Centre
PATH=/s/chopin/a/grad/asharifi/usr/bin/bin:./include/:/s/chopin/a/grad/asharifi/usr/.openmpi/bin/:/s/chopin/a/grad/asharifi/usr/.openmpi/bin/:/s/chopin/a/grad/asharifi/
usr/bin/bin/:./bin/:/s/chopin/a/grad/asharifi/usr/bin/:../include:./sparsehash/m4:./sparsehash/lib:./sparsehash:/usr/local/anaconda3-4.4.0/bin:../openmpi-2.1.5/bin:./sp
arsehash/:./openmpi-2.1.5/bin/:/usr/local/anaconda/bin/:/usr/local/anaconda/bin/:/s/chopin/a/grad/asharifi/bioconda/bin:/usr/local/cuda_8.0.61-cudnnv5/bin:/s/chopin/a/g
rad/asharifi/.nvm/versions/node/v7.5.0/bin:/s/chopin/a/grad/asharifi/bin:/s/chopin/a/grad/asharifi/e/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/s/damavand/e/asha
rifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin:.:/s/chopin/a/grad/asharifi/anaconda3/bin:/usr/local/anaconda/bin/:/usr/local/anaconda/bin/:/s/chopin/a/grad
/asharifi/bioconda/bin:/usr/local/cuda_8.0.61-cudnnv5/bin:/s/chopin/a/grad/asharifi/bin:/s/chopin/a/grad/asharifi/e/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/s/
damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin:.:/opt/local/bin:/opt/local/sbin:~/f/miniconda3/bin:/usr/local/anaconda/bin/:/usr/local/anaco
nda/bin/:/s/chopin/a/grad/asharifi/bioconda/bin:/usr/local/cuda_8.0.61-cudnnv5/bin:/s/chopin/a/grad/asharifi/bin:/s/chopin/a/grad/asharifi/e/bin:/bin:/usr/bin:/sbin:/us
r/sbin:/usr/local/bin:/s/damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin:.:/s/chopin/a/grad/asharifi/anaconda3/bin:/usr/local/anaconda/bin/:/
usr/local/anaconda/bin/:/s/chopin/a/grad/asharifi/bioconda/bin:/usr/local/cuda_8.0.61-cudnnv5/bin:/s/chopin/a/grad/asharifi/bin:/s/chopin/a/grad/asharifi/e/bin:/bin:/us
r/bin:/sbin:/usr/sbin:/usr/local/bin:/s/damavand/e/asharifi/BS_Aligners/methylcode/bench/gsnap/gmap-2014-12-06/bin:.:/opt/local/bin:/opt/local/sbin:~/f/miniconda3/bin:/
usr/lib64/qt-3.3/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/s/chopin/a/grad/asharifi/.composer/vendor/bin:/s/chopin/a/grad/asharifi/bin:/s
/chopin/a/grad/asharifi/S:/s/chopin/a/grad/asharifi/.local/bin:/s/chopin/a/grad/asharifi/e/Applications/weblogo:/s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux
64/bin:/s/chopin/a/grad/asharifi/f/miniconda3/bin:/s/chopin/a/grad/asharifi/e/Applications/Torch/bin:/usr/local/torch/install/bin:/s/chopin/a/grad/asharifi/f/Saberi/pg/
gsutil:/s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/bin:/s/chopin/a/grad/asharifi/f/miniconda3/bin:/s/chopin/a/grad/asharifi/e/Applications/Torch/bin:/usr
/local/torch/install/bin:/s/chopin/a/grad/asharifi/f/Saberi/pg/gsutil:/s/chopin/a/grad/asharifi/bin:/s/chopin/a/grad/asharifi/S:/s/chopin/a/grad/asharifi/.local/bin:/s/
chopin/a/grad/asharifi/e/Applications/weblogo:/s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/bin:/s/chopin/a/grad/asharifi/f/miniconda3/bin:/s/chopin/a/grad
/asharifi/e/Applications/Torch/bin:/usr/local/torch/install/bin:/s/chopin/a/grad/asharifi/f/Saberi/pg/gsutil:/s/chopin/a/grad/asharifi/e/Applications/gurobi652/linux64/
bin:/s/chopin/a/grad/asharifi/f/miniconda3/bin:/s/chopin/a/grad/asharifi/e/Applications/Torch/bin:/usr/local/torch/install/bin:/s/chopin/a/grad/asharifi/f/Saberi/pg/gsu
til
ABYSS (ABySS) 2.1.4
Written by Jared Simpson, Shaun Jackman and Anthony Raymond.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

zsh:1: command not found: ABYSS-P
make: [/s/chopin/a/grad/asharifi/usr/bin/bin/abyss-pe:406: versions] Error 127 (ignored)
AdjList (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

DistanceEst (ABySS) 2.1.4
Written by Jared Simpson and Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

MergeContigs (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

MergePaths (ABySS) 2.1.4
Written by Jared Simpson and Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

Overlap (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

PathConsensus (ABySS) 2.1.4
Written by Shaun Jackman and Rong She.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

PathOverlap (ABySS) 2.1.4
Written by Shaun Jackman and Tony Raymond.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

PopBubbles (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

SimpleGraph (ABySS) 2.1.4
Written by Jared Simpson and Shaun Jackman.

Copyright 2018 Canada's Michael Smith Genome Sciences Centre

abyss-fac (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

abyss-filtergraph (ABySS) 2.1.4
Written by Tony Raymond.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

abyss-fixmate (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

abyss-map (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

abyss-scaffold (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2018 Canada's Michael Smith Genome Sciences Centre

abyss-sealer (ABySS) 2.1.4
Written by Shaun Jackman, Hamid Mohamadi, Anthony Raymond,
Ben Vandervalk and Daniel Paulino

Copyright 2014 Canada's Michael Smith Genome Science Centre

abyss-todot (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

abyss-map (ABySS) 2.1.4
Written by Shaun Jackman.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

GNU Awk 4.1.4, API: 1.1 (GNU MPFR 3.1.6-p2, GNU MP 6.1.2)
Copyright (C) 1989, 1991-2016 Free Software Foundation.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/.

sort (GNU coreutils) 8.27
Copyright (C) 2017 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Mike Haertel and Paul Eggert.

mpirun (Open MPI) 2.1.5

Report bugs to http://www.open-mpi.org/community/help/
(base) [04:38 asharifi@oak: ~/usr/bin/bin]$ cd
(base) [04:50 asharifi@oak: ~]$ cd usr/lib/openmpi/
(base) [04:50 asharifi@oak: ~/usr/lib/openmpi]$ ls
libompi_dbg_msgq.la      mca_dfs_orted.so             mca_filem_raw.la         mca_osc_pt2pt.so          mca_rmaps_resilient.la      mca_sharedfp_sm.so
libompi_dbg_msgq.so      mca_dfs_test.la              mca_filem_raw.so         mca_osc_rdma.la           mca_rmaps_resilient.so      mca_shmem_mmap.la
mca_allocator_basic.la   mca_dfs_test.so              mca_fs_ufs.la            mca_osc_rdma.so           mca_rmaps_round_robin.la    mca_shmem_mmap.so
mca_allocator_basic.so   mca_errmgr_default_app.la    mca_fs_ufs.so            mca_osc_sm.la             mca_rmaps_round_robin.so    mca_shmem_posix.la
mca_allocator_bucket.la  mca_errmgr_default_app.so    mca_grpcomm_direct.la    mca_osc_sm.so             mca_rmaps_seq.la            mca_shmem_posix.so
mca_allocator_bucket.so  mca_errmgr_default_hnp.la    mca_grpcomm_direct.so    mca_patcher_overwrite.la  mca_rmaps_seq.so            mca_shmem_sysv.la
mca_atomic_basic.la      mca_errmgr_default_hnp.so    mca_iof_hnp.la           mca_patcher_overwrite.so  mca_rmaps_staged.la         mca_shmem_sysv.so
mca_atomic_basic.so      mca_errmgr_default_orted.la  mca_iof_hnp.so           mca_plm_isolated.la       mca_rmaps_staged.so         mca_spml_yoda.la
mca_bml_r2.la            mca_errmgr_default_orted.so  mca_iof_mr_hnp.la        mca_plm_isolated.so       mca_rml_oob.la              mca_spml_yoda.so
mca_bml_r2.so            mca_errmgr_default_tool.la   mca_iof_mr_hnp.so        mca_plm_rsh.la            mca_rml_oob.so              mca_sshmem_mmap.la
mca_btl_self.la          mca_errmgr_default_tool.so   mca_iof_mr_orted.la      mca_plm_rsh.so            mca_routed_binomial.la      mca_sshmem_mmap.so
mca_btl_self.so          mca_ess_env.la               mca_iof_mr_orted.so      mca_plm_slurm.la          mca_routed_binomial.so      mca_sshmem_sysv.la
mca_btl_sm.la            mca_ess_env.so               mca_iof_orted.la         mca_plm_slurm.so          mca_routed_debruijn.la      mca_sshmem_sysv.so
mca_btl_sm.so            mca_ess_hnp.la               mca_iof_orted.so         mca_pmix_pmix112.la       mca_routed_debruijn.so      mca_state_app.la
mca_btl_tcp.la           mca_ess_hnp.so               mca_iof_tool.la          mca_pmix_pmix112.so       mca_routed_direct.la        mca_state_app.so
mca_btl_tcp.so           mca_ess_pmi.la               mca_iof_tool.so          mca_pml_cm.la             mca_routed_direct.so        mca_state_dvm.la
mca_btl_vader.la         mca_ess_pmi.so               mca_io_ompio.la          mca_pml_cm.so             mca_routed_radix.la         mca_state_dvm.so
mca_btl_vader.so         mca_ess_singleton.la         mca_io_ompio.so          mca_pml_ob1.la            mca_routed_radix.so         mca_state_hnp.la
mca_coll_basic.la        mca_ess_singleton.so         mca_io_romio314.la       mca_pml_ob1.so            mca_rtc_freq.la             mca_state_hnp.so
mca_coll_basic.so        mca_ess_slurm.la             mca_io_romio314.so       mca_pstat_linux.la        mca_rtc_freq.so             mca_state_novm.la
mca_coll_inter.la        mca_ess_slurm.so             mca_memheap_buddy.la     mca_pstat_linux.so        mca_rtc_hwloc.la            mca_state_novm.so
mca_coll_inter.so        mca_ess_tool.la              mca_memheap_buddy.so     mca_ras_loadleveler.la    mca_rtc_hwloc.so            mca_state_orted.la
mca_coll_libnbc.la       mca_ess_tool.so              mca_memheap_ptmalloc.la  mca_ras_loadleveler.so    mca_schizo_ompi.la          mca_state_orted.so
mca_coll_libnbc.so       mca_fbtl_posix.la            mca_memheap_ptmalloc.so  mca_ras_simulator.la      mca_schizo_ompi.so          mca_state_staged_hnp.la
mca_coll_self.la         mca_fbtl_posix.so            mca_mpool_hugepage.la    mca_ras_simulator.so      mca_scoll_basic.la          mca_state_staged_hnp.so
mca_coll_self.so         mca_fcoll_dynamic_gen2.la    mca_mpool_hugepage.so    mca_ras_slurm.la          mca_scoll_basic.so          mca_state_staged_orted.la
mca_coll_sm.la           mca_fcoll_dynamic_gen2.so    mca_notifier_syslog.la   mca_ras_slurm.so          mca_scoll_mpi.la            mca_state_staged_orted.so
mca_coll_sm.so           mca_fcoll_dynamic.la         mca_notifier_syslog.so   mca_rcache_grdma.la       mca_scoll_mpi.so            mca_state_tool.la
mca_coll_sync.la         mca_fcoll_dynamic.so         mca_odls_default.la      mca_rcache_grdma.so       mca_sec_basic.la            mca_state_tool.so
mca_coll_sync.so         mca_fcoll_individual.la      mca_odls_default.so      mca_rmaps_mindist.la      mca_sec_basic.so            mca_topo_basic.la
mca_coll_tuned.la        mca_fcoll_individual.so      mca_oob_tcp.la           mca_rmaps_mindist.so      mca_sharedfp_individual.la  mca_topo_basic.so
mca_coll_tuned.so        mca_fcoll_static.la          mca_oob_tcp.so           mca_rmaps_ppr.la          mca_sharedfp_individual.so  mca_vprotocol_pessimist.la
mca_dfs_app.la           mca_fcoll_static.so          mca_oob_usock.la         mca_rmaps_ppr.so          mca_sharedfp_lockedfile.la  mca_vprotocol_pessimist.so
mca_dfs_app.so           mca_fcoll_two_phase.la       mca_oob_usock.so         mca_rmaps_rank_file.la    mca_sharedfp_lockedfile.so
mca_dfs_orted.la         mca_fcoll_two_phase.so       mca_osc_pt2pt.la         mca_rmaps_rank_file.so    mca_sharedfp_sm.la
(base) [04:50 asharifi@oak: ~/usr/lib/openmpi]$ ls ..
libmca_common_sm.la          libmpi.so.20                         libompitrace.la          libopen-rte.so.20                 mpi_f08_interfaces.mod
libmca_common_sm.so          libmpi.so.20.10.3                    libompitrace.so          libopen-rte.so.20.10.4            mpi_f08.mod
libmca_common_sm.so.20       libmpi_usempif08.la                  libompitrace.so.20       liboshmem.la                      mpi_f08_types.mod
libmca_common_sm.so.20.10.1  libmpi_usempif08.so                  libompitrace.so.20.10.0  liboshmem.so                      mpi.mod
libmpi.la                    libmpi_usempif08.so.20               libopen-pal.la           liboshmem.so.20                   openmpi
libmpi_mpifh.la              libmpi_usempif08.so.20.11.1          libopen-pal.so           liboshmem.so.20.10.3              pkgconfig
libmpi_mpifh.so              libmpi_usempi_ignore_tkr.la          libopen-pal.so.20        mpi_ext.mod                       pmpi_f08_interfaces.mod
libmpi_mpifh.so.20           libmpi_usempi_ignore_tkr.so          libopen-pal.so.20.10.4   mpi_f08_callbacks.mod             rstudio
libmpi_mpifh.so.20.12.1      libmpi_usempi_ignore_tkr.so.20       libopen-rte.la           mpi_f08_ext.mod
libmpi.so                    libmpi_usempi_ignore_tkr.so.20.11.1  libopen-rte.so           mpi_f08_interfaces_callbacks.mod

(base) [05:24 asharifi@oak: /s/oak/c/nobackup/asharifi/Mostafa/Applications/openmpi-2.1.5/lib/openmpi]$ ls
libompi_dbg_msgq.la      mca_dfs_orted.so             mca_filem_raw.la         mca_osc_pt2pt.so          mca_rmaps_resilient.la      mca_sharedfp_sm.so
libompi_dbg_msgq.so      mca_dfs_test.la              mca_filem_raw.so         mca_osc_rdma.la           mca_rmaps_resilient.so      mca_shmem_mmap.la
mca_allocator_basic.la   mca_dfs_test.so              mca_fs_ufs.la            mca_osc_rdma.so           mca_rmaps_round_robin.la    mca_shmem_mmap.so
mca_allocator_basic.so   mca_errmgr_default_app.la    mca_fs_ufs.so            mca_osc_sm.la             mca_rmaps_round_robin.so    mca_shmem_posix.la
mca_allocator_bucket.la  mca_errmgr_default_app.so    mca_grpcomm_direct.la    mca_osc_sm.so             mca_rmaps_seq.la            mca_shmem_posix.so
mca_allocator_bucket.so  mca_errmgr_default_hnp.la    mca_grpcomm_direct.so    mca_patcher_overwrite.la  mca_rmaps_seq.so            mca_shmem_sysv.la
mca_atomic_basic.la      mca_errmgr_default_hnp.so    mca_iof_hnp.la           mca_patcher_overwrite.so  mca_rmaps_staged.la         mca_shmem_sysv.so
mca_atomic_basic.so      mca_errmgr_default_orted.la  mca_iof_hnp.so           mca_plm_isolated.la       mca_rmaps_staged.so         mca_spml_yoda.la
mca_bml_r2.la            mca_errmgr_default_orted.so  mca_iof_mr_hnp.la        mca_plm_isolated.so       mca_rml_oob.la              mca_spml_yoda.so
mca_bml_r2.so            mca_errmgr_default_tool.la   mca_iof_mr_hnp.so        mca_plm_rsh.la            mca_rml_oob.so              mca_sshmem_mmap.la
mca_btl_self.la          mca_errmgr_default_tool.so   mca_iof_mr_orted.la      mca_plm_rsh.so            mca_routed_binomial.la      mca_sshmem_mmap.so
mca_btl_self.so          mca_ess_env.la               mca_iof_mr_orted.so      mca_plm_slurm.la          mca_routed_binomial.so      mca_sshmem_sysv.la
mca_btl_sm.la            mca_ess_env.so               mca_iof_orted.la         mca_plm_slurm.so          mca_routed_debruijn.la      mca_sshmem_sysv.so
mca_btl_sm.so            mca_ess_hnp.la               mca_iof_orted.so         mca_pmix_pmix112.la       mca_routed_debruijn.so      mca_state_app.la
mca_btl_tcp.la           mca_ess_hnp.so               mca_iof_tool.la          mca_pmix_pmix112.so       mca_routed_direct.la        mca_state_app.so
mca_btl_tcp.so           mca_ess_pmi.la               mca_iof_tool.so          mca_pml_cm.la             mca_routed_direct.so        mca_state_dvm.la
mca_btl_vader.la         mca_ess_pmi.so               mca_io_ompio.la          mca_pml_cm.so             mca_routed_radix.la         mca_state_dvm.so
mca_btl_vader.so         mca_ess_singleton.la         mca_io_ompio.so          mca_pml_ob1.la            mca_routed_radix.so         mca_state_hnp.la
mca_coll_basic.la        mca_ess_singleton.so         mca_io_romio314.la       mca_pml_ob1.so            mca_rtc_freq.la             mca_state_hnp.so
mca_coll_basic.so        mca_ess_slurm.la             mca_io_romio314.so       mca_pstat_linux.la        mca_rtc_freq.so             mca_state_novm.la
mca_coll_inter.la        mca_ess_slurm.so             mca_memheap_buddy.la     mca_pstat_linux.so        mca_rtc_hwloc.la            mca_state_novm.so
mca_coll_inter.so        mca_ess_tool.la              mca_memheap_buddy.so     mca_ras_loadleveler.la    mca_rtc_hwloc.so            mca_state_orted.la
mca_coll_libnbc.la       mca_ess_tool.so              mca_memheap_ptmalloc.la  mca_ras_loadleveler.so    mca_schizo_ompi.la          mca_state_orted.so
mca_coll_libnbc.so       mca_fbtl_posix.la            mca_memheap_ptmalloc.so  mca_ras_simulator.la      mca_schizo_ompi.so          mca_state_staged_hnp.la
mca_coll_self.la         mca_fbtl_posix.so            mca_mpool_hugepage.la    mca_ras_simulator.so      mca_scoll_basic.la          mca_state_staged_hnp.so
mca_coll_self.so         mca_fcoll_dynamic_gen2.la    mca_mpool_hugepage.so    mca_ras_slurm.la          mca_scoll_basic.so          mca_state_staged_orted.la
mca_coll_sm.la           mca_fcoll_dynamic_gen2.so    mca_notifier_syslog.la   mca_ras_slurm.so          mca_scoll_mpi.la            mca_state_staged_orted.so
mca_coll_sm.so           mca_fcoll_dynamic.la         mca_notifier_syslog.so   mca_rcache_grdma.la       mca_scoll_mpi.so            mca_state_tool.la
mca_coll_sync.la         mca_fcoll_dynamic.so         mca_odls_default.la      mca_rcache_grdma.so       mca_sec_basic.la            mca_state_tool.so
mca_coll_sync.so         mca_fcoll_individual.la      mca_odls_default.so      mca_rmaps_mindist.la      mca_sec_basic.so            mca_topo_basic.la
mca_coll_tuned.la        mca_fcoll_individual.so      mca_oob_tcp.la           mca_rmaps_mindist.so      mca_sharedfp_individual.la  mca_topo_basic.so
mca_coll_tuned.so        mca_fcoll_static.la          mca_oob_tcp.so           mca_rmaps_ppr.la          mca_sharedfp_individual.so  mca_vprotocol_pessimist.la
mca_dfs_app.la           mca_fcoll_static.so          mca_oob_usock.la         mca_rmaps_ppr.so          mca_sharedfp_lockedfile.la  mca_vprotocol_pessimist.so
mca_dfs_app.so           mca_fcoll_two_phase.la       mca_oob_usock.so         mca_rmaps_rank_file.la    mca_sharedfp_lockedfile.so
mca_dfs_orted.la         mca_fcoll_two_phase.so       mca_osc_pt2pt.la         mca_rmaps_rank_file.so    mca_sharedfp_sm.la

make

make  all-recursive
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'
Making all in bin
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/bin'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/bin'
Making all in doc
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/doc'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/doc'
Making all in Common
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Common'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-ContigID.o -MD -MP -MF .deps/l
ibcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/l
ibcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Histogram.o -MD -MP -MF .deps/
libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Kmer.o -MD -MP -MF .deps/libco
mmon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
mv -f .deps/libcommon_a-Kmer.Tpo .deps/libcommon_a-Kmer.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Log.o -MD -MP -MF .deps/libcom
mon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Options.o -MD -MP -MF .deps/li
bcommon_a-Options.Tpo -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Sequence.o -MD -MP -MF .deps/l
ibcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-SignalHandler.o -MD -MP -MF .d
eps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Timer.o -MD -MP -MF .deps/libc
ommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
mv -f .deps/libcommon_a-Timer.Tpo .deps/libcommon_a-Timer.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-Uncompress.o -MD -MP -MF .deps
/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libcommon_a-city.o -MD -MP -MF .deps/libco
mmon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po
rm -f libcommon.a
ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence
.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o
ranlib libcommon.a
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Common'
Making all in Graph
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Graph'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_gc-gc.o -MD -MP -MF .dep
s/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_todot-todot.o -MD -MP -M
F .deps/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
mv -f .deps/abyss_todot-todot.Tpo .deps/abyss_todot-todot.Po
g++ -Wall -Wextra -g -O2 -L. -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Graph'
Making all in DataLayer
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataLayer'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libdatalayer_a-FastaReader.o -MD -MP -MF .
deps/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libdatalayer_a-FastaWriter.o -MD -MP -MF .
deps/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
ranlib libdatalayer.a
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_fac-fac.o -MD -MP -MF .deps/abyss_fa
c-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
mv -f .deps/abyss_fac-fac.Tpo .deps/abyss_fac-fac.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_tofastq-abyss-tofastq.o -MD -MP -MF
.deps/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -l
m
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataLayer'
Making all in DataBase
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataBase'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libdb_a-DB.o -MD -MP -MF .deps/libdb_a-DB.
Tpo -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ranlib libdb.a
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_db_csv-DB.o -MD -MP -MF .deps/abyss_
db_csv-DB.Tpo -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
mv -f .deps/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_db_csv-db-csv.o -MD -MP -MF .deps/ab
yss_db_csv-db-csv.Tpo -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
mv -f .deps/abyss_db_csv-db-csv.Tpo .deps/abyss_db_csv-db-csv.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataBase'
Making all in FMIndex
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FMIndex'
g++ -DHAVE_CONFIG_H -I. -I..  -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopi
n/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libfmindex_a-bit_array.o -MD -MP -M
F .deps/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
mv -f .deps/libfmindex_a-bit_array.Tpo .deps/libfmindex_a-bit_array.Po
rm -f libfmindex.a
ar cru libfmindex.a libfmindex_a-bit_array.o
ranlib libfmindex.a
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_count-count.o -MD -MP -M
F .deps/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
mv -f .deps/abyss_count-count.Tpo .deps/abyss_count-count.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_dawg-abyss-dawg.o -MD -M
P -MF .deps/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
mv -f .deps/abyss_dawg-abyss-dawg.Tpo .deps/abyss_dawg-abyss-dawg.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FMIndex'
Making all in Assembly
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Assembly'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libassembly_a-AssemblyAlgorithms.o -MD -MP
 -MF .deps/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc
mv -f .deps/libassembly_a-AssemblyAlgorithms.Tpo .deps/libassembly_a-AssemblyAlgorithms.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libassembly_a-Options.o -MD -MP -MF .deps/
libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc
mv -f .deps/libassembly_a-Options.Tpo .deps/libassembly_a-Options.Po
rm -f libassembly.a
ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a
ranlib libassembly.a
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Assembly'
Making all in dialign
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/dialign'
depbase=`echo alig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT alig.o -MD -MP -MF $depbase.Tpo -c -o alig.o alig.c &&\
mv -f $depbase.Tpo $depbase.Po
alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined
 extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
                    ^~~~~~~~~~~~~~
alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined
 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
                    ^~~~~~~~~~~
depbase=`echo assemble.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT assemble.o -MD -MP -MF $depbase.Tpo -c -o assemble.o assemb
le.c &&\
mv -f $depbase.Tpo $depbase.Po
assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined
 extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
                    ^~~~~~~~~~
assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined
 extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
                                ^~~~~~~~
assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined
 extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,
                                       ^~~~~~~~~~~~~~~~~
assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined
 extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
                    ^~~~~~~~~~~~~~
assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined
 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
                    ^~~~~~~~~~~
depbase=`echo diag.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT diag.o -MD -MP -MF $depbase.Tpo -c -o diag.o diag.c &&\
mv -f $depbase.Tpo $depbase.Po
diag.c:1456:3: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static
   real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
   ^~~~~~~~~~~~~~~~
depbase=`echo io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT io.o -MD -MP -MF $depbase.Tpo -c -o io.o io.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo orf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT orf.o -MD -MP -MF $depbase.Tpo -c -o orf.o orf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo parameters.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT parameters.o -MD -MP -MF $depbase.Tpo -c -o parameters.o pa
rameters.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo prob.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT prob.o -MD -MP -MF $depbase.Tpo -c -o prob.o prob.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo translate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT translate.o -MD -MP -MF $depbase.Tpo -c -o translate.o tran
slate.c &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libdialign.a
ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
ranlib libdialign.a
depbase=`echo museq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0  -g -O2 -MT museq.o -MD -MP -MF $depbase.Tpo -c -o museq.o museq.c &&\
mv -f $depbase.Tpo $depbase.Po
museq.c: In function ‘main’:
museq.c:168:2: warning: implicit declaration of function ‘free_diag’; did you mean ‘free_diag_col’? [-Wimplicit-function-declaration]
  free_diag(adcol.diags[i]);
  ^~~~~~~~~
  free_diag_col
museq.c:278:27: warning: implicit declaration of function ‘free_alignment’ [-Wimplicit-function-declaration]
     if(! para->FAST_MODE) free_alignment(algn);
                           ^~~~~~~~~~~~~~
gcc  -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o dialign museq.o libdialign.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/dialign'
Making all in Align
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Align'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libalign_a-alignGlobal.o -MD -
MP -MF .deps/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
mv -f .deps/libalign_a-alignGlobal.Tpo .deps/libalign_a-alignGlobal.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libalign_a-dialign.o -MD -MP -
MF .deps/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
mv -f .deps/libalign_a-dialign.Tpo .deps/libalign_a-dialign.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libalign_a-dna_diag_prob.o -MD
 -MP -MF .deps/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
mv -f .deps/libalign_a-dna_diag_prob.Tpo .deps/libalign_a-dna_diag_prob.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT libalign_a-smith_waterman.o -M
D -MP -MF .deps/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
mv -f .deps/libalign_a-smith_waterman.Tpo .deps/libalign_a-smith_waterman.Po
rm -f libalign.a
ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
ranlib libalign.a
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_
align-align.o -MD -MP -MF .deps/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
mv -f .deps/abyss_align-align.Tpo .deps/abyss_align-align.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLay
er/libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_
mergepairs-mergepairs.o -MD -MP -MF .deps/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
mv -f .deps/abyss_mergepairs-mergepairs.Tpo .deps/abyss_mergepairs-mergepairs.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdiali
gn.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Align'
Making all in ABYSS
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ABYSS'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/gra
d/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT ABYSS-abyss.o -MD -MP -MF .deps/ABYSS-abys
s.Tpo -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
mv -f .deps/ABYSS-abyss.Tpo .deps/ABYSS-abyss.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Assembly/libassembly.a ..
/DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ABYSS'
Making all in Bloom
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Bloom'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_
bloom-bloom.o -MD -MP -MF .deps/abyss_bloom-bloom.Tpo -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
mv -f .deps/abyss_bloom-bloom.Tpo .deps/abyss_bloom-bloom.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a
 ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Bloom'
Making all in BloomDBG
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/BloomDBG'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_
bloom_dbg-bloom-dbg.o -MD -MP -MF .deps/abyss_bloom_dbg-bloom-dbg.Tpo -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
mv -f .deps/abyss_bloom_dbg-bloom-dbg.Tpo .deps/abyss_bloom_dbg-bloom-dbg.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Comm
on/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/BloomDBG'
Making all in Konnector
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Konnector'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT konnec
tor-konnector.o -MD -MP -MF .deps/konnector-konnector.Tpo -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a
 ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Konnector'
Making all in Consensus
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Consensus'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT Consensus-Conse
nsus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
mv -f .deps/Consensus-Consensus.Tpo .deps/Consensus-Consensus.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -
lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Consensus'
Making all in DAssembler
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DAssembler'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT DAssembler-DAss
embler.o -MD -MP -MF .deps/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
mv -f .deps/DAssembler-DAssembler.Tpo .deps/DAssembler-DAssembler.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT DAssembler-Rota
tedRead.o -MD -MP -MF .deps/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
mv -f .deps/DAssembler-RotatedRead.Tpo .deps/DAssembler-RotatedRead.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a
../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DAssembler'
Making all in DistanceEst
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DistanceEst'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT DistanceEst-DistanceE
st.o -MD -MP -MF .deps/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
mv -f .deps/DistanceEst-DistanceEst.Tpo .deps/DistanceEst-DistanceEst.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT DistanceEst-MLE.o -MD
 -MP -MF .deps/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
mv -f .deps/DistanceEst-MLE.Tpo .deps/DistanceEst-MLE.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -ls
qlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openm
pi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT Dis
tanceEst_ssq-DistanceEst.o -MD -MP -MF .deps/DistanceEst_ssq-DistanceEst.Tpo -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
mv -f .deps/DistanceEst_ssq-DistanceEst.Tpo .deps/DistanceEst_ssq-DistanceEst.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openm
pi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT Dis
tanceEst_ssq-MLE.o -MD -MP -MF .deps/DistanceEst_ssq-MLE.Tpo -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
mv -f .deps/DistanceEst_ssq-MLE.Tpo .deps/DistanceEst_ssq-MLE.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase
/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DistanceEst'
Making all in KAligner
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/KAligner'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT KAligner-KAlign
er.o -MD -MP -MF .deps/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
mv -f .deps/KAligner-KAligner.Tpo .deps/KAligner-KAligner.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT KAligner-Aligne
r.o -MD -MP -MF .deps/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
mv -f .deps/KAligner-Aligner.Tpo .deps/KAligner-Aligner.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/li
bcommon.a -lpthread -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/KAligner'
Making all in Layout
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Layout'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_layout-layout.o -MD -MP
-MF .deps/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc
mv -f .deps/abyss_layout-layout.Tpo .deps/abyss_layout-layout.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Layout'
Making all in LogKmerCount
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/LogKmerCount'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT logcou
nter-logcounter.o -MD -MP -MF .deps/logcounter-logcounter.Tpo -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc
mv -f .deps/logcounter-logcounter.Tpo .deps/logcounter-logcounter.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalig
n.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/LogKmerCount'
Making all in Map
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Map'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr
/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT ab
yss_index-index.o -MD -MP -MF .deps/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
mv -f .deps/abyss_index-index.Tpo .deps/abyss_index-index.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../C
ommon/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr
/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -
O2 -MT abyss_map-map.o -MD -MP -MF .deps/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
mv -f .deps/abyss_map-map.Tpo .deps/abyss_map-map.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a .
./Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a
/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -We
xtra -fopenmp -g -O2 -MT abyss_map_ssq-map.o -MD -MP -MF .deps/abyss_map_ssq-map.Tpo -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc
mv -f .deps/abyss_map_ssq-map.Tpo .deps/abyss_map_ssq-map.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatal
ayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr
/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -
O2 -MT abyss_overlap-overlap.o -MD -MP -MF .deps/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
mv -f .deps/abyss_overlap-overlap.Tpo .deps/abyss_overlap-overlap.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libd
atalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Map'
Making all in MergePaths
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/MergePaths'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT MergeP
aths-MergePaths.o -MD -MP -MF .deps/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
mv -f .deps/MergePaths-MergePaths.Tpo .deps/MergePaths-MergePaths.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../D
ataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/l
ib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT Merg
eContigs-MergeContigs.o -MD -MP -MF .deps/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
mv -f .deps/MergeContigs-MergeContigs.Tpo .deps/MergeContigs-MergeContigs.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Data
Layer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/gr
ad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextr
a -g -O2 -MT PathConsensus-PathConsensus.o -MD -MP -MF .deps/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo '.
/'`PathConsensus.cpp
mv -f .deps/PathConsensus-PathConsensus.Tpo .deps/PathConsensus-PathConsensus.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../D
ataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/MergePaths'
Making all in Misc
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Misc'
ghc --make -O2 -hidir ./ -odir ./ -o abyss-samtobreak samtobreak.hs
[1 of 1] Compiling Main             ( samtobreak.hs, Main.o )
Linking abyss-samtobreak ...
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Misc'
Making all in Overlap
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Overlap'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT Overlap-Overlap
.o -MD -MP -MF .deps/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
mv -f .deps/Overlap-Overlap.Tpo .deps/Overlap-Overlap.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Overlap'
Making all in PairedDBG
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PairedDBG'
depbase=`echo KmerPair.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..   -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/as
harifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT KmerPair.o -MD -MP -MF $depbase.Tpo -c -o Kmer
Pair.o KmerPair.cc &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libpaireddbg.a
ar cru libpaireddbg.a KmerPair.o
ranlib libpaireddbg.a
g++ -DHAVE_CONFIG_H -I. -I..  -DPAIRED_DBG -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s
/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_paired_dbg-abyss-paired
-dbg.o -MD -MP -MF .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc
mv -f .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo .deps/abyss_paired_dbg-abyss-paired-dbg.Po
g++ -DHAVE_CONFIG_H -I. -I..  -DPAIRED_DBG -I.. -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s
/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_paired_dbg-KmerPair.o -
MD -MP -MF .deps/abyss_paired_dbg-KmerPair.Tpo -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
mv -f .deps/abyss_paired_dbg-KmerPair.Tpo .deps/abyss_paired_dbg-KmerPair.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Asse
mbly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PairedDBG'
Making all in ParseAligns
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ParseAligns'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_fixmate-abyss-fixmate.o
-MD -MP -MF .deps/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
mv -f .deps/abyss_fixmate-abyss-fixmate.Tpo .deps/abyss_fixmate-abyss-fixmate.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../C
ommon/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openm
pi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_fixmat
e_ssq-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixma
te.cc
mv -f .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo .deps/abyss_fixmate_ssq-abyss-fixmate.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -
lm  ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT ParseAligns-ParseAligns.o -MD
-MP -MF .deps/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
mv -f .deps/ParseAligns-ParseAligns.Tpo .deps/ParseAligns-ParseAligns.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ParseAligns'
Making all in PathOverlap
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PathOverlap'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT PathOverlap-Pat
hOverlap.o -MD -MP -MF .deps/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp
mv -f .deps/PathOverlap-PathOverlap.Tpo .deps/PathOverlap-PathOverlap.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLay
er/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PathOverlap'
Making all in PopBubbles
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PopBubbles'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/l
ib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2
 -MT PopBubbles-PopBubbles.o -MD -MP -MF .deps/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp
mv -f .deps/PopBubbles-PopBubbles.Tpo .deps/PopBubbles-PopBubbles.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalig
n.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PopBubbles'
Making all in Scaffold
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Scaffold'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_scaffold-scaffo
ld.o -MD -MP -MF .deps/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc
mv -f .deps/abyss_scaffold-scaffold.Tpo .deps/abyss_scaffold-scaffold.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm
  ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_junction-juncti
on.o -MD -MP -MF .deps/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
mv -f .deps/abyss_junction-junction.Tpo .deps/abyss_junction-junction.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_longseqdist-lon
gseqdist.o -MD -MP -MF .deps/abyss_longseqdist-longseqdist.Tpo -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
mv -f .deps/abyss_longseqdist-longseqdist.Tpo .deps/abyss_longseqdist-longseqdist.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -l
m
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT abyss_drawgraph-drawgraph.o -M
D -MP -MF .deps/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc
mv -f .deps/abyss_drawgraph-drawgraph.Tpo .deps/abyss_drawgraph-drawgraph.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Scaffold'
Making all in SimpleGraph
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/SimpleGraph'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/include   -I/s/
chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -g -O2 -MT SimpleGra
ph-SimpleGraph.o -MD -MP -MF .deps/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp
mv -f .deps/SimpleGraph-SimpleGraph.Tpo .deps/SimpleGraph-SimpleGraph.Po
g++ -Wall -Wextra -Wno-strict-aliasing -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3
 -ldl -lm  ../Common/libcommon.a -lpthread -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/SimpleGraph'
Making all in kmerprint
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/kmerprint'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Assembly -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/us
r/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT k
merprint-kmerprint.o -MD -MP -MF .deps/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc
mv -f .deps/kmerprint-kmerprint.Tpo .deps/kmerprint-kmerprint.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ..
/Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/kmerprint'
Making all in FilterGraph
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FilterGraph'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_
filtergraph-FilterGraph.o -MD -MP -MF .deps/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.c
c
mv -f .deps/abyss_filtergraph-FilterGraph.Tpo .deps/abyss_filtergraph-FilterGraph.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a .
./Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FilterGraph'
Making all in GapFiller
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/GapFiller'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/g
rad/asharifi/usr/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wext
ra -fopenmp -g -O2 -MT abyss_gapfill-gapfill.o -MD -MP -MF .deps/abyss_gapfill-gapfill.Tpo -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
mv -f .deps/abyss_gapfill-gapfill.Tpo .deps/abyss_gapfill-gapfill.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign
.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/GapFiller'
Making all in Sealer
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Sealer'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr/lib/openmpi/
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -MT abyss_
sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 [820/9097]
sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
mv -f .deps/abyss_sealer-sealer.Tpo .deps/abyss_sealer-sealer.Po
g++ -Wall -Wextra -fopenmp -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalig
n.a ../Common/libcommon.a -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Sealer'
Making all in AdjList
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/AdjList'
g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/s/chopin/a/grad/asharifi/mostafa/Applications/abyss  -isystem/s/chopin/a/grad/asharifi/usr
/lib/openmpi/include   -I/s/chopin/a/grad/asharifi/usr/bin/include -isystem/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT Ad
jList-AdjList.o -MD -MP -MF .deps/AdjList-AdjList.Tpo -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp
mv -f .deps/AdjList-AdjList.Tpo .deps/AdjList-AdjList.Po
g++ -Wall -Wextra -g -O2  -L/s/chopin/a/grad/asharifi/usr/lib/openmpi/lib    -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG
/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/AdjList'
Making all in lib/bloomfilter
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/bloomfilter'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/bloomfilter'
Making all in lib/nthash
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/nthash'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/nthash'
Making all in lib/gtest-1.7.0
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/gtest-1.7.0'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/gtest-1.7.0'
Making all in Unittest
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Unittest'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Unittest'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'
pandoc -s -o README.html README.md
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'

make install

Making install in bin
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/bin'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/bin'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
 /bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk a$
  /bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk ab
yss-dida '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/bin'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/bin'
Making install in doc
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/doc'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/doc'
make[2]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/share/doc/abyss'
 /bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/s/chopin/a/grad/asharifi/usr/bin/share/doc/abyss'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/share/man/man1'
 /bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/s/chopin/a/grad/asharifi/usr/bin/share/man/man1'
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/doc'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/doc'
Making install in Common
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Common'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Common'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Common'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Common'
Making install in Graph
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Graph'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Graph'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-gc abyss-todot '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Graph'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Graph'
Making install in DataLayer
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataLayer'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataLayer'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-fac abyss-tofastq '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataLayer'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataLayer'
Making install in DataBase
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataBase'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataBase'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-db-csv '/s/chopin/a/grad/asharifi/usr/bin/bin'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
 /bin/install -c abyss-db-txt '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataBase'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DataBase'
Making install in FMIndex
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FMIndex'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FMIndex'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FMIndex'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FMIndex'
Making install in Assembly
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Assembly'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Assembly'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Assembly'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Assembly'
Making install in dialign
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/dialign'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/dialign'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/dialign'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/dialign'
Making install in Align
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Align'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Align'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-align abyss-mergepairs '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Align'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Align'
Making install in ABYSS
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ABYSS'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ABYSS'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c ABYSS '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ABYSS'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ABYSS'
Making install in Bloom
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Bloom'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Bloom'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-bloom '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Bloom'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Bloom'
Making install in BloomDBG
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/BloomDBG'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/BloomDBG'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-bloom-dbg '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/BloomDBG'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/BloomDBG'
Making install in Konnector
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Konnector'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Konnector'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c konnector '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Konnector'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Konnector'
Making install in Consensus
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Consensus'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Consensus'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c Consensus '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Consensus'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Consensus'
Making install in DAssembler
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DAssembler'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DAssembler'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c DAssembler '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DAssembler'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DAssembler'
Making install in DistanceEst
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DistanceEst'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DistanceEst'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c DistanceEst DistanceEst-ssq '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DistanceEst'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/DistanceEst'
Making install in KAligner
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/KAligner'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/KAligner'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c KAligner '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/KAligner'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/KAligner'
Making install in Layout
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Layout'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Layout'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-layout '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Layout'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Layout'
Making install in LogKmerCount
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/LogKmerCount'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/LogKmerCount'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c logcounter '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/LogKmerCount'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/LogKmerCount'
Making install in Map
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Map'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Map'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Map'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Map'
Making install in MergePaths
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/MergePaths'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/MergePaths'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c MergePaths MergeContigs PathConsensus '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/MergePaths'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/MergePaths'
Making install in Misc
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Misc'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Misc'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-samtobreak '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Misc'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Misc'
Making install in Overlap
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Overlap'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Overlap'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c Overlap '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Overlap'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Overlap'
Making install in PairedDBG
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PairedDBG'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PairedDBG'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-paired-dbg '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PairedDBG'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PairedDBG'
Making install in ParseAligns
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ParseAligns'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ParseAligns'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ParseAligns'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/ParseAligns'
Making install in PathOverlap
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PathOverlap'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PathOverlap'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c PathOverlap '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PathOverlap'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PathOverlap'
Making install in PopBubbles
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PopBubbles'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PopBubbles'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c PopBubbles '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PopBubbles'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/PopBubbles'
Making install in Scaffold
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Scaffold'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Scaffold'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Scaffold'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Scaffold'
Making install in SimpleGraph
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/SimpleGraph'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/SimpleGraph'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c SimpleGraph '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/SimpleGraph'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/SimpleGraph'
Making install in kmerprint
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/kmerprint'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/kmerprint'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/kmerprint'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/kmerprint'
Making install in FilterGraph
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FilterGraph'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FilterGraph'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-filtergraph '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FilterGraph'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/FilterGraph'
Making install in GapFiller
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/GapFiller'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/GapFiller'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-gapfill '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/GapFiller'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/GapFiller'
Making install in Sealer
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Sealer'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Sealer'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c abyss-sealer '/s/chopin/a/grad/asharifi/usr/bin/bin'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/share/man/man1'
 /bin/install -c -m 644 abyss-sealer.1 '/s/chopin/a/grad/asharifi/usr/bin/share/man/man1'
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Sealer'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Sealer'
Making install in AdjList
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/AdjList'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/AdjList'
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/bin'
  /bin/install -c AdjList '/s/chopin/a/grad/asharifi/usr/bin/bin'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/AdjList'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/AdjList'
Making install in lib/bloomfilter
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/bloomfilter'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/bloomfilter'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/bloomfilter'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/bloomfilter'
Making install in lib/nthash
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/nthash'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/nthash'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/nthash'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/nthash'
Making install in lib/gtest-1.7.0
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/gtest-1.7.0'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/gtest-1.7.0'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/gtest-1.7.0'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/lib/gtest-1.7.0'
Making install in Unittest
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Unittest'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Unittest'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Unittest'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss/Unittest'
make[1]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'
make[2]: Entering directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'
make[2]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/s/chopin/a/grad/asharifi/usr/bin/share/doc/abyss'
 /bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md README.html '/s/chopin/a/grad/asharifi/usr/bin/share/doc/abyss'
make[2]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'
make[1]: Leaving directory '/s/chopin/a/grad/asharifi/mostafa/Applications/abyss'

Out Logs

 ./configure --prefix=/s/chopin/a/grad/asharifi/usr/bin CPPFLAGS=-I/s/chopin/a/grad/asharifi/usr/bin/include -
-with-mpi=/s/chopin/a/grad/asharifi/usr/lib/openmpi
********************************************************
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for ranlib... ranlib
checking for ghc... ghc
The Glorious Glasgow Haskell Compilation System, version 8.0.2
checking for pandoc... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for std::hash<int>... yes
checking for std::tr1::hash<int>... yes
checking for std::tr1::tuple<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking if compiler needs -Werror to reject unknown flags... no
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... g++ -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... yes
checking tr1/functional presence... yes
checking for tr1/functional... yes
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... yes
checking google/sparse_hash_map presence... yes
checking for google/sparse_hash_map... yes
checking unordered_map usability... yes
checking unordered_map presence... yes
checking for unordered_map... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for g++ option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Misc/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating lib/gtest-1.7.0/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating lib/bloomfilter/Makefile
config.status: creating lib/nthash/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

Run Commands

(base) [05:09 asharifi@oak: ~/mostafa]$ abyss-pe mpirun='mpirun --mca btl sm' v=-v k=96 np=24 name=DjPG2103 lr='lra' lra=../data/barcoded.fastq
mpirun --mca btl sm -np 24 ABYSS-P -k96 -q3 -v   --coverage-hist=coverage.hist -s DjPG2103-bubbles.fa  -o DjPG2103-1.fa ../data/barcoded.fastq
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
      line parameter option (remember that mpirun interprets the first
      unrecognized command line token as the executable).

Node:       oak
Executable: ABYSS-P
--------------------------------------------------------------------------
24 total processes failed to start
make: *** [/s/chopin/a/grad/asharifi/usr/bin/bin/abyss-pe:548: DjPG2103-1.fa] Error 134


(base) [05:10 asharifi@oak: ~/mostafa]$ abyss-pe mpirun='/s/chopin/a/grad/asharifi/usr/.openmpi/bin/mpirun --mca btl sm' v=-v k=96 np=24 name=DjPG2103 lr='lra' lra=../d
ata/barcoded.fastq
/s/chopin/a/grad/asharifi/usr/.openmpi/bin/mpirun --mca btl sm -np 24 ABYSS-P -k96 -q3 -v   --coverage-hist=coverage.hist -s DjPG2103-bubbles.fa  -o DjPG2103-1.fa ../da
ta/barcoded.fastq
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
      line parameter option (remember that mpirun interprets the first
      unrecognized command line token as the executable).

Node:       oak
Executable: ABYSS-P
--------------------------------------------------------------------------
24 total processes failed to start
make: *** [/s/chopin/a/grad/asharifi/usr/bin/bin/abyss-pe:548: DjPG2103-1.fa] Error 134