Based on the 'Quick installation instructions' in section #2 of 'Userguide.pdf' that comes in the unpacked version of http://eddylab.org/software/hmmer/hmmer-2.3.2.tar.gz.
# Get the software
!curl -OL http://eddylab.org/software/hmmer/hmmer-2.3.2.tar.gz
# unpack it
!tar xzf hmmer-2.3.2.tar.gz
# go into unpacked software directory
%cd hmmer-2.3.2
# Configure for this system, and build the programs
! ./configure
!make
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1000k 100 1000k 0 0 4370k 0 --:--:-- --:--:-- --:--:-- 4370k /home/jovyan/demo/hmmer-2.3.2 configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for x86_64-conda-linux-gnu-gcc... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc accepts -g... yes checking for /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc option to accept ANSI C... none needed checking for x86_64-conda-linux-gnu-ranlib... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ranlib checking for ar... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ar checking build system type... x86_64-conda-linux-gnu checking host system type... x86_64-conda-linux-gnu checking whether your make is GNU make... yes, it is. checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: creating src/config.h configure: configuring in squid configure: running /bin/bash './configure' --prefix=/usr/local 'CC=/srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib' 'build_alias=x86_64-conda-linux-gnu' 'host_alias=x86_64-conda-linux-gnu' --cache-file=/dev/null --srcdir=. configure: configuring the SQUID library for your system. checking for x86_64-conda-linux-gnu-gcc... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc accepts -g... yes checking for /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc option to accept ANSI C... none needed checking for x86_64-conda-linux-gnu-ranlib... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ranlib checking for ar... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ar checking whether your make is GNU make... yes, it is. checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking how to run the C preprocessor... /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cpp checking for egrep... 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 for unsigned short... yes checking size of unsigned short... 2 checking for unsigned int... yes checking size of unsigned int... 4 checking for unsigned long... yes checking size of unsigned long... 8 checking for unsigned long long... yes checking size of unsigned long long... 8 checking for strtoul... yes checking for strtoull... yes checking whether fpos_t is an arithmetic datatype... no. checking for strtoull... (cached) yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for stat64... yes checking for struct stat64... no! checking for off_t... yes checking size of off_t... 8 checking for off64_t... no checking size of off64_t... 0 checking for fpos_t... yes checking size of fpos_t... 16 configure: creating ./config.status config.status: creating Makefile config.status: creating Testsuite/Makefile config.status: creating squid.h config.status: creating squidconf.h make[1]: Entering directory '/home/jovyan/demo/hmmer-2.3.2/squid' /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c afetch_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c a2m.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c aligneval.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c alignio.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c clustal.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c cluster.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c dayhoff.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c eps.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c file.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c getopt.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c gki.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c gsi.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c hsregex.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c iupac.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c msa.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c msf.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c phylip.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c revcomp.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c rk.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c selex.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c seqencode.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c shuffle.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sqerror.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sqio.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c squidcore.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sre_ctype.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sre_math.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sre_random.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sre_string.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c ssi.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c stack.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c stockholm.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c stopwatch.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c translate.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c types.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c vectorops.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c weight.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o afetch afetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c alistat_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o alistat alistat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c compalign_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o compalign compalign_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c compstruct_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o compstruct compstruct_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c revcomp_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o revcomp revcomp_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c seqsplit_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o seqsplit seqsplit_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c seqstat_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o seqstat seqstat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sfetch_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o sfetch sfetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c shuffle_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o shuffle shuffle_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sindex_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o sindex sindex_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c sreformat_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o sreformat sreformat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c translate_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o translate translate_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -c weight_main.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o weight weight_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ar rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o a - a2m.o a - aligneval.o a - alignio.o a - clustal.o a - cluster.o a - dayhoff.o a - eps.o a - file.o a - getopt.o a - gki.o a - gsi.o a - hsregex.o a - iupac.o a - msa.o a - msf.o a - phylip.o a - revcomp.o a - rk.o a - selex.o a - seqencode.o a - shuffle.o a - sqerror.o a - sqio.o a - squidcore.o a - sre_ctype.o a - sre_math.o a - sre_random.o a - sre_string.o a - ssi.o a - stack.o a - stockholm.o a - stopwatch.o a - translate.o a - types.o a - vectorops.o a - weight.o /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ranlib libsquid.a chmod 644 libsquid.a make[1]: Leaving directory '/home/jovyan/demo/hmmer-2.3.2/squid' make[1]: Entering directory '/home/jovyan/demo/hmmer-2.3.2/squid' make[1]: Nothing to be done for 'module'. make[1]: Leaving directory '/home/jovyan/demo/hmmer-2.3.2/squid' make[1]: Entering directory '/home/jovyan/demo/hmmer-2.3.2/src' /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmalign.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c alphabet.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c core_algorithms.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c debug.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c display.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c emit.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c emulation.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c fast_algorithms.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c histogram.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmio.c hmmio.c: In function 'WriteBinHMM': hmmio.c:488:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(v20magic), sizeof(unsigned int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:492:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->flags), sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:496:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->M), sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:497:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(Alphabet_type), sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:498:32: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] if (hmm->flags & PLAN7_RF) fwrite((char *) hmm->rf, sizeof(char), hmm->M+1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:499:32: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] if (hmm->flags & PLAN7_CS) fwrite((char *) hmm->cs, sizeof(char), hmm->M+1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:500:32: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] if (hmm->flags & PLAN7_MAP) fwrite((char *) hmm->map, sizeof(int), hmm->M+1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:502:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->nseq), sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:504:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->checksum), sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:506:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->ga1), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:507:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->ga2), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:510:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->tc1), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:511:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->tc2), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:514:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->nc1), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:515:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->nc2), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:520:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->xt[k], sizeof(float), 2, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:523:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *)&(hmm->p1), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:524:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->null, sizeof(float), Alphabet_size, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:528:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->mu), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:529:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &(hmm->lambda), sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:534:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *)&(hmm->tbd1),sizeof(float), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:535:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->begin, sizeof(float), hmm->M+1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:536:3: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->end, sizeof(float), hmm->M+1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:541:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->mat[k], sizeof(float), Alphabet_size, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:543:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->ins[k], sizeof(float), Alphabet_size, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:545:5: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) hmm->t[k], sizeof(float), 7, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c: In function 'write_bin_string': hmmio.c:1339:7: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &len, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:1340:7: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) s, sizeof(char), len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmio.c:1345:7: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite((char *) &len, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c mathsupport.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c masks.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c misc.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c modelmakers.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c plan7.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c plan9.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c postprob.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c prior.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c pvm.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c threads.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c tophits.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c trace.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmbuild.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmcalibrate.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmconvert.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmemit.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmfetch.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmindex.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmpfam.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -c hmmsearch.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -L../squid -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm make[1]: Leaving directory '/home/jovyan/demo/hmmer-2.3.2/src' make[1]: Entering directory '/home/jovyan/demo/hmmer-2.3.2/src' /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-ranlib libhmmer.a chmod 644 libhmmer.a make[1]: Leaving directory '/home/jovyan/demo/hmmer-2.3.2/src' make[1]: Entering directory '/home/jovyan/demo/hmmer-2.3.2/testsuite' /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c alignalign_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o alignalign_test -L../squid -L../src alignalign_test.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c evd_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o evd_test -L../squid -L../src evd_test.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c masks_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o masks_test -L../squid -L../src masks_test.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c parsingviterbi_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o parsingviterbi_test -L../squid -L../src parsingviterbi_test.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c tophits_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o tophits_test -L../squid -L../src tophits_test.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c trace_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o trace_test -L../squid -L../src trace_test.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c viterbi_exercise.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o viterbi_exercise -L../squid -L../src viterbi_exercise.o -lhmmer -lsquid -lm /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /srv/conda/envs/notebook/include -DHAVE_CONFIG_H -I../squid -I../src -c weeviterbi_test.c /srv/conda/envs/notebook/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /srv/conda/envs/notebook/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/srv/conda/envs/notebook/lib -Wl,-rpath-link,/srv/conda/envs/notebook/lib -L/srv/conda/envs/notebook/lib -DHAVE_CONFIG_H -o weeviterbi_test -L../squid -L../src weeviterbi_test.o -lhmmer -lsquid -lm make[1]: Leaving directory '/home/jovyan/demo/hmmer-2.3.2/testsuite'
Add the OP's provided example data to be converted, from the bottom of https://www.biostars.org/p/9500884/#9500951 .
s='''ID 002L_FRG3G Reviewed; 320 AA.
AC Q6GZX3;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 05-JUN-2019, entry version 38.
DE RecName: Full=Uncharacterized protein 002L;
GN ORFNames=FV3-002L;
OS Frog virus 3 (isolate Goorha) (FV-3).
OC Viruses; Iridoviridae; Alphairidovirinae; Ranavirus.
OX NCBI_TaxID=654924;
OH NCBI_TaxID=8295; Ambystoma (mole salamanders).
OH NCBI_TaxID=30343; Dryophytes versicolor (chameleon treefrog).
OH NCBI_TaxID=8404; Lithobates pipiens (Northern leopard frog) (Rana pipiens).
OH NCBI_TaxID=8316; Notophthalmus viridescens (Eastern newt) (Triturus viridescens).
OH NCBI_TaxID=45438; Rana sylvatica (Wood frog).
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15165820; DOI=10.1016/j.virol.2004.02.019;
RA Tan W.G., Barkman T.J., Gregory Chinchar V., Essani K.;
RT "Comparative genomic analyses of frog virus 3, type species of the
RT genus Ranavirus (family Iridoviridae).";
RL Virology 323:70-84(2004).
CC -!- SUBCELLULAR LOCATION: Host membrane {ECO:0000305}; Single-pass
CC membrane protein {ECO:0000305}.
DR EMBL; AY548484; AAT09661.1; -; Genomic_DNA.
DR RefSeq; YP_031580.1; NC_005946.1.
DR GeneID; 2947774; -.
DR KEGG; vg:2947774; -.
DR Proteomes; UP000008770; Genome.
DR GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR InterPro; IPR004251; Pox_virus_G9/A16.
DR Pfam; PF03003; Pox_G9-A16; 1.
PE 4: Predicted;
KW Complete proteome; Host membrane; Membrane; Reference proteome;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1 320 Uncharacterized protein 002L.
FT /FTId=PRO_0000410509.
FT TRANSMEM 301 318 Helical. {ECO:0000255}.
FT COMPBIAS 263 295 Pro-rich.
SQ SEQUENCE 320 AA; 34642 MW; 9E110808B6E328E0 CRC64;
MSIIGATRLQ NDKSDTYSAG PCYAGGCSAF TPRGTCGKDW DLGEQTCASG FCTSQPLCAR
IKKTQVCGLR YSSKGKDPLV SAEWDSRGAP YVRCTYDADL IDTQAQVDQF VSMFGESPSL
AERYCMRGVK NTAGELVSRV SSDADPAGGW CRKWYSAHRG PDQDAALGSF CIKNPGAADC
KCINRASDPV YQKVKTLHAY PDQCWYVPCA ADVGELKMGT QRDTPTNCPT QVCQIVFNML
DDGSVTMDDV KNTINCDFSK YVPPPPPPKP TPPTPPTPPT PPTPPTPPTP PTPRPVHNRK
VMFFVAGAVL VAILISTVRW
//
ID 012L_FRG3G Reviewed; 297 AA.
AC Q6GZW3;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 05-JUN-2019, entry version 29.
DE RecName: Full=Uncharacterized protein 012L;
GN ORFNames=FV3-012L;
OS Frog virus 3 (isolate Goorha) (FV-3).
OC Viruses; Iridoviridae; Alphairidovirinae; Ranavirus.
OX NCBI_TaxID=654924;
OH NCBI_TaxID=8295; Ambystoma (mole salamanders).
OH NCBI_TaxID=30343; Dryophytes versicolor (chameleon treefrog).
OH NCBI_TaxID=8404; Lithobates pipiens (Northern leopard frog) (Rana pipiens).
OH NCBI_TaxID=8316; Notophthalmus viridescens (Eastern newt) (Triturus viridescens).
OH NCBI_TaxID=45438; Rana sylvatica (Wood frog).
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15165820; DOI=10.1016/j.virol.2004.02.019;
RA Tan W.G., Barkman T.J., Gregory Chinchar V., Essani K.;
RT "Comparative genomic analyses of frog virus 3, type species of the
RT genus Ranavirus (family Iridoviridae).";
RL Virology 323:70-84(2004).
DR EMBL; AY548484; AAT09671.1; -; Genomic_DNA.
DR RefSeq; YP_031590.1; NC_005946.1.
DR GeneID; 2947784; -.
DR KEGG; vg:2947784; -.
DR Proteomes; UP000008770; Genome.
PE 4: Predicted;
KW Complete proteome; Reference proteome.
FT CHAIN 1 297 Uncharacterized protein 012L.
FT /FTId=PRO_0000410530.
SQ SEQUENCE 297 AA; 32669 MW; 9B1D9247FF7E5D25 CRC64;
MCAKLVEMAF GPVNADSPPL TAEEKESAVE KLVGSKPFPA LKKKYHDKVP AQDPKYCLFS
FVEVLPSCDI KAAGAEEMCS CCIKRRRGQV FGVACVRGTA HTLAKAKQKA DKLVGDYDSV
HVVQTCHVGR PFPLVSSGMA QETVAPSAME AAEAAMDAKS AEKRKERMRQ KLEMRKREQE
IKARNRKLLE DPSCDPDAEE ETDLERYATL RVKTTCLLEN AKNASAQIKE YLASMRKSAE
AVVAMEAADP TLVENYPGLI RDSRAKMGVS KQDTEAFLKM SSFDCLTAAS ELETMGF
//
ID 015R_FRG3G Reviewed; 322 AA.
AC Q6GZW0;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 05-JUN-2019, entry version 40.
DE RecName: Full=Uncharacterized protein 015R;
GN ORFNames=FV3-015R;
OS Frog virus 3 (isolate Goorha) (FV-3).
OC Viruses; Iridoviridae; Alphairidovirinae; Ranavirus.
OX NCBI_TaxID=654924;
OH NCBI_TaxID=8295; Ambystoma (mole salamanders).
OH NCBI_TaxID=30343; Dryophytes versicolor (chameleon treefrog).
OH NCBI_TaxID=8404; Lithobates pipiens (Northern leopard frog) (Rana pipiens).
OH NCBI_TaxID=8316; Notophthalmus viridescens (Eastern newt) (Triturus viridescens).
OH NCBI_TaxID=45438; Rana sylvatica (Wood frog).
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15165820; DOI=10.1016/j.virol.2004.02.019;
RA Tan W.G., Barkman T.J., Gregory Chinchar V., Essani K.;
RT "Comparative genomic analyses of frog virus 3, type species of the
RT genus Ranavirus (family Iridoviridae).";
RL Virology 323:70-84(2004).
DR EMBL; AY548484; AAT09674.1; -; Genomic_DNA.
DR RefSeq; YP_031593.1; NC_005946.1.
DR PRIDE; Q6GZW0; -.
DR GeneID; 2947735; -.
DR KEGG; vg:2947735; -.
DR Proteomes; UP000008770; Genome.
DR InterPro; IPR027417; P-loop_NTPase.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 4: Predicted;
KW Complete proteome; Reference proteome.
FT CHAIN 1 322 Uncharacterized protein 015R.
FT /FTId=PRO_0000410504.
SQ SEQUENCE 322 AA; 36098 MW; 8E5F5B3DA9CDFF8A CRC64;
MEQVPIKEMR LSDLRPNNKS IDTDLGGTKL VVIGKPGSGK STLIKALLDS KRHIIPCAVV
ISGSEEANGF YKGVVPDLFI YHQFSPSIID RIHRRQVKAK AEMGSKKSWL LVVIDDCMDN
AKMFNDKEVR ALFKNGRHWN VLVVIANQYV MDLTPDLRSS VDGVFLFREN NVTYRDKTYA
NFASVVPKKL YPTVMETVCQ NYRCMFIDNT KATDNWHDSV FWYKAPYSKS AVAPFGARSY
WKYACSKTGE EMPAVFDNVK ILGDLLLKEL PEAGEALVTY GGKDGPSDNE DGPSDDEDGP
SDDEEGLSKD GVSEYYQSDL DD
//
ID 023R_IIV3 Reviewed; 106 AA.
AC Q197D7;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2006, sequence version 1.
DT 18-SEP-2019, entry version 20.
DE RecName: Full=Uncharacterized protein 023R;
GN ORFNames=IIV3-023R;
OS Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).
OC Viruses; Iridoviridae; Betairidovirinae; Chloriridovirus.
OX NCBI_TaxID=345201;
OH NCBI_TaxID=7163; Aedes vexans (Inland floodwater mosquito) (Culex vexans).
OH NCBI_TaxID=42431; Culex territans.
OH NCBI_TaxID=332058; Culiseta annulata.
OH NCBI_TaxID=310513; Ochlerotatus sollicitans (eastern saltmarsh mosquito).
OH NCBI_TaxID=329105; Ochlerotatus taeniorhynchus (Black salt marsh mosquito) (Aedes taeniorhynchus).
OH NCBI_TaxID=7183; Psorophora ferox.
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16912294; DOI=10.1128/jvi.00464-06;
RA Delhon G., Tulman E.R., Afonso C.L., Lu Z., Becnel J.J., Moser B.A.,
RA Kutish G.F., Rock D.L.;
RT "Genome of invertebrate iridescent virus type 3 (mosquito iridescent
RT virus).";
RL J. Virol. 80:8439-8449(2006).
DR EMBL; DQ643392; ABF82053.1; -; Genomic_DNA.
DR RefSeq; YP_654595.1; NC_008187.1.
DR GeneID; 4156230; -.
DR KEGG; vg:4156230; -.
DR OrthoDB; 16183at10239; -.
DR Proteomes; UP000001358; Genome.
PE 4: Predicted;
KW Complete proteome; Reference proteome.
FT CHAIN 1 106 Uncharacterized protein 023R.
FT /FTId=PRO_0000377945.
SQ SEQUENCE 106 AA; 12767 MW; 6620465F6FC52A18 CRC64;
MGSYMLFDSL IKLVENRNPL NHEQKLWLID VINNTLNLEG KEKLYSLLIV HNKQQTKIYD
PKEPFYDIEK IPVQLQLVWY EFTKMHLKSQ NEDRRRKMSL YAGRSP
//
ID 048L_FRG3G Reviewed; 83 AA.
AC Q6GZS8;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 05-JUN-2019, entry version 27.
DE RecName: Full=Uncharacterized protein 048L;
GN ORFNames=FV3-048L;
OS Frog virus 3 (isolate Goorha) (FV-3).
OC Viruses; Iridoviridae; Alphairidovirinae; Ranavirus.
OX NCBI_TaxID=654924;
OH NCBI_TaxID=8295; Ambystoma (mole salamanders).
OH NCBI_TaxID=30343; Dryophytes versicolor (chameleon treefrog).
OH NCBI_TaxID=8404; Lithobates pipiens (Northern leopard frog) (Rana pipiens).
OH NCBI_TaxID=8316; Notophthalmus viridescens (Eastern newt) (Triturus viridescens).
OH NCBI_TaxID=45438; Rana sylvatica (Wood frog).
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15165820; DOI=10.1016/j.virol.2004.02.019;
RA Tan W.G., Barkman T.J., Gregory Chinchar V., Essani K.;
RT "Comparative genomic analyses of frog virus 3, type species of the
RT genus Ranavirus (family Iridoviridae).";
RL Virology 323:70-84(2004).
DR EMBL; AY548484; AAT09707.1; -; Genomic_DNA.
DR RefSeq; YP_031626.1; NC_005946.1.
DR GeneID; 2947827; -.
DR KEGG; vg:2947827; -.
DR Proteomes; UP000008770; Genome.
PE 4: Predicted;
KW Complete proteome; Reference proteome.
FT CHAIN 1 83 Uncharacterized protein 048L.
FT /FTId=PRO_0000410516.
SQ SEQUENCE 83 AA; 9566 MW; 52A13E9E325273F6 CRC64;
MTAKTLDPSD YNVRDDSTTG MFTPVDRFVC DPESDRIIVR KIPPEWTIGN SMRFVHFTKE
FTQTFDPSES PSNIVRHTNG KKK
//'''
%store s >seq_file.txt
Writing 's' (str) to file 'seq_file.txt'.
!pwd
/home/jovyan/demo/hmmer-2.3.2
sreformat
¶# go into squid directory
%cd squid
/home/jovyan/demo/hmmer-2.3.2/squid
sreformat
¶!./sreformat -h
sreformat - convert between sequence formats SQUID 1.9g (January 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Usage: sreformat [-options] <format> <seqfile> Output format choices: Unaligned Aligned ----------- ------- fasta stockholm embl msf genbank a2m gcg phylip gcgdata clustal pir selex raw eps Available options are: -h : help; print brief help on version and usage -d : force DNA alphabet for nucleic acid sequence -r : force RNA alphabet for nucleic acid sequence -l : force lower case -u : force upper case -x : convert non-IUPAC chars in DNA to N's for IUPAC/BLAST compatibility Expert options: --informat <s>: input sequence file is in format <s> --mingap : remove columns containing all gaps (seqfile=alignment) --nogap : remove columns containing any gaps (seqfile=alignment) --pfam : modify Stockholm format output to be in PFAM style (1 line/seq) --sam : try to convert gaps to SAM style (seqfile=alignment) --samfrac <x> : convert to SAM convention; cols w/ gapfrac > x are inserts --gapsym <c> : convert all gaps to character '<c>'
#copy the sequence file to the directory we are in.
!cp ../seq_file.txt .
!./sreformat fasta seq_file.txt
>002L_FRG3G RecName: Full=Uncharacterized protein 002L; MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASG FCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADL IDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGW CRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAY PDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDV KNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRK VMFFVAGAVLVAILISTVRW >012L_FRG3G RecName: Full=Uncharacterized protein 012L; MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVP AQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTA HTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAME AAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEE ETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADP TLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF >015R_FRG3G RecName: Full=Uncharacterized protein 015R; MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDS KRHIIPCAVVISGSEEANGFYKGVVPDLFIYHQFSPSIIDRIHRRQVKAK AEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYV MDLTPDLRSSVDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQ NYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSYWKYACSKTGE EMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGP SDDEEGLSKDGVSEYYQSDLDD >023R_IIV3 RecName: Full=Uncharacterized protein 023R; MGSYMLFDSLIKLVENRNPLNHEQKLWLIDVINNTLNLEGKEKLYSLLIV HNKQQTKIYDPKEPFYDIEKIPVQLQLVWYEFTKMHLKSQNEDRRRKMSL YAGRSP >048L_FRG3G RecName: Full=Uncharacterized protein 048L; MTAKTLDPSDYNVRDDSTTGMFTPVDRFVCDPESDRIIVRKIPPEWTIGN SMRFVHFTKEFTQTFDPSESPSNIVRHTNGKKK
Send the converted output to a file.
!./sreformat fasta seq_file.txt > seq_file.fa
Display contents of converted file.
!cat seq_file.fa
>002L_FRG3G RecName: Full=Uncharacterized protein 002L; MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASG FCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADL IDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGW CRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAY PDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDV KNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRK VMFFVAGAVLVAILISTVRW >012L_FRG3G RecName: Full=Uncharacterized protein 012L; MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVP AQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTA HTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAME AAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEE ETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADP TLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF >015R_FRG3G RecName: Full=Uncharacterized protein 015R; MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDS KRHIIPCAVVISGSEEANGFYKGVVPDLFIYHQFSPSIIDRIHRRQVKAK AEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYV MDLTPDLRSSVDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQ NYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSYWKYACSKTGE EMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGP SDDEEGLSKDGVSEYYQSDLDD >023R_IIV3 RecName: Full=Uncharacterized protein 023R; MGSYMLFDSLIKLVENRNPLNHEQKLWLIDVINNTLNLEGKEKLYSLLIV HNKQQTKIYDPKEPFYDIEKIPVQLQLVWYEFTKMHLKSQNEDRRRKMSL YAGRSP >048L_FRG3G RecName: Full=Uncharacterized protein 048L; MTAKTLDPSDYNVRDDSTTGMFTPVDRFVCDPESDRIIVRKIPPEWTIGN SMRFVHFTKEFTQTFDPSESPSNIVRHTNGKKK
sreformat
via Python¶import os
os.system("./sreformat fasta seq_file.txt > made_by_python_seq_file.fa");
!cat made_by_python_seq_file.fa
>002L_FRG3G RecName: Full=Uncharacterized protein 002L; MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASG FCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADL IDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGW CRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAY PDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDV KNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRK VMFFVAGAVLVAILISTVRW >012L_FRG3G RecName: Full=Uncharacterized protein 012L; MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVP AQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTA HTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAME AAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEE ETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADP TLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF >015R_FRG3G RecName: Full=Uncharacterized protein 015R; MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDS KRHIIPCAVVISGSEEANGFYKGVVPDLFIYHQFSPSIIDRIHRRQVKAK AEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYV MDLTPDLRSSVDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQ NYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSYWKYACSKTGE EMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGP SDDEEGLSKDGVSEYYQSDLDD >023R_IIV3 RecName: Full=Uncharacterized protein 023R; MGSYMLFDSLIKLVENRNPLNHEQKLWLIDVINNTLNLEGKEKLYSLLIV HNKQQTKIYDPKEPFYDIEKIPVQLQLVWYEFTKMHLKSQNEDRRRKMSL YAGRSP >048L_FRG3G RecName: Full=Uncharacterized protein 048L; MTAKTLDPSDYNVRDDSTTGMFTPVDRFVCDPESDRIIVRKIPPEWTIGN SMRFVHFTKEFTQTFDPSESPSNIVRHTNGKKK
Python script provided hugo.avila and GenoMax, see https://www.biostars.org/p/9500884/#9500990 . (It has been edited in the string here to escape the \n
symbols.)
ss='''import os
import sys
import re
def main(input_fname: str, output_fname: str) -> None:
with open(output_fname, 'w') as f_out:
with open(input_fname, 'r') as f_in:
for record in re.split('//', f_in.read())[:-1]:
record_id = re.split('\s+', record[record.index('ID'):])[1]
sequence = ''.join(record[record.index('SQ'):].split('\\n')[1:]).replace(' ','')
f_out.write(f'>{record_id}\\n{sequence}\\n')
if __name__ == '__main__':
main(input_fname=sys.argv[1], output_fname=sys.argv[2])'''
%store ss >script.py
Writing 'ss' (str) to file 'script.py'.
%run script.py seq_file.txt made_by_purepython_seq_file.fa
You'd replace %run
with your typical call to Python if you are running this on the command line. So perhaps:
python script.py seq_file.txt made_by_purepython_seq_file.fa
Or,
python3 script.py seq_file.txt made_by_purepython_seq_file.fa
Or recommended for Windows machines,
py script.py seq_file.txt made_by_purepython_seq_file.fa
Let's see if that worked.
!cat made_by_purepython_seq_file.fa
>002L_FRG3G MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADLIDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGWCRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAYPDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDVKNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRKVMFFVAGAVLVAILISTVRW >012L_FRG3G MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVPAQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTAHTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAMEAAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEEETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADPTLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF >015R_FRG3G MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDSKRHIIPCAVVISGSEEANGFYKGVVPDLFIYHQFSPSIIDRIHRRQVKAKAEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYVMDLTPDLRSSVDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQNYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSYWKYACSKTGEEMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGPSDDEEGLSKDGVSEYYQSDLDD >023R_IIV3 MGSYMLFDSLIKLVENRNPLNHEQKLWLIDVINNTLNLEGKEKLYSLLIVHNKQQTKIYDPKEPFYDIEKIPVQLQLVWYEFTKMHLKSQNEDRRRKMSLYAGRSP >048L_FRG3G MTAKTLDPSDYNVRDDSTTGMFTPVDRFVCDPESDRIIVRKIPPEWTIGNSMRFVHFTKEFTQTFDPSESPSNIVRHTNGKKK
hugo.avila's script from https://www.biostars.org/p/9500884/#9501206 (It has been edited in the string here to escape the \n symbols.)
ss2='''
import sys
import re
def main(input_fname: str, output_fname: str) -> None:
with open(output_fname, 'w') as f_out:
with open(input_fname, 'r') as f_in:
# The input file is separated with '//' so if we split the file by these caracters
# it is possible to get a list of records that can by looped:
# "record1//record2//record//" --split('//')--> ["record1", "record2", "record3", ""].
# As you can see above the last item of the splitted string is a "" (empty string)
# so we need to ignore it
# li like this: ["record1", "record2", "record3", ""][:-1] -> ["record1", "record2", "record3"].
for record in re.split('//', f_in.read())[:-1]:
# I cant see way the first code only returned the first id, i did run it and it worked for the sample.
# I think that must be some format error in one of the sequences. This try block is kind of
# ugly but it wil go to the end of your file, write the output and print the unformated records (if any).
try:
# split a record into a list of lines and get only the one that starts with 'ID'.
# I think that maybe u only want the whole line so i did not pull only the id.
id_line = list(filter(lambda x: x.startswith('ID'), record.split('\\n')))[0]
sequence = ''.join(record[record.index('SQ'):].split('\\n')[1:]).replace(' ','')
f_out.write(f'>{id_line}\\n{sequence}\\n')
except Exception as e:
print (f'Unformated record\\n{record}')
pass
if __name__ == '__main__':
main(input_fname=sys.argv[1], output_fname=sys.argv[2])'''
%store ss2 >scriptalt.py
Writing 'ss2' (str) to file 'scriptalt.py'.
%run scriptalt.py seq_file.txt made_by_purepython2_seq_file.fa
You'd replace %run
with your typical call to Python if you are running this on the command line. So perhaps:
python scriptalt.py seq_file.txt made_by_purepython2_seq_file.fa
Or,
python3 scriptalt.py seq_file.txt made_by_purepython2_seq_file.fa
Or recommended for Windows machines,
py script.py seq_file.txt made_by_purepython_seq_file.fa
Let's see if that worked.
!cat made_by_purepython2_seq_file.fa
>ID 002L_FRG3G Reviewed; 320 AA. MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADLIDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGWCRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAYPDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDVKNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRKVMFFVAGAVLVAILISTVRW >ID 012L_FRG3G Reviewed; 297 AA. MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVPAQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTAHTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAMEAAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEEETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADPTLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF >ID 015R_FRG3G Reviewed; 322 AA. MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDSKRHIIPCAVVISGSEEANGFYKGVVPDLFIYHQFSPSIIDRIHRRQVKAKAEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYVMDLTPDLRSSVDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQNYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSYWKYACSKTGEEMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGPSDDEEGLSKDGVSEYYQSDLDD >ID 023R_IIV3 Reviewed; 106 AA. MGSYMLFDSLIKLVENRNPLNHEQKLWLIDVINNTLNLEGKEKLYSLLIVHNKQQTKIYDPKEPFYDIEKIPVQLQLVWYEFTKMHLKSQNEDRRRKMSLYAGRSP >ID 048L_FRG3G Reviewed; 83 AA. MTAKTLDPSDYNVRDDSTTGMFTPVDRFVCDPESDRIIVRKIPPEWTIGNSMRFVHFTKEFTQTFDPSESPSNIVRHTNGKKK
Enjoy!