RUFUS
RUFUS copied to clipboard
Published
20 hours ago •
jandrewrfarrell
jandrewrfarrell
testRun failure
Trying to build RUFUS with gcc version
[moldach@cedar1 TOOL_TMP_DIR]$ wget https://github.com/jandrewrfarrell/RUFUS/archive/V1.0.tar.gz
--2021-01-29 11:44:34-- https://github.com/jandrewrfarrell/RUFUS/archive/V1.0.tar.gz
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/jandrewrfarrell/RUFUS/tar.gz/V1.0 [following]
--2021-01-29 11:44:34-- https://codeload.github.com/jandrewrfarrell/RUFUS/tar.gz/V1.0
Resolving codeload.github.com (codeload.github.com)... 140.82.114.9
Connecting to codeload.github.com (codeload.github.com)|140.82.114.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘V1.0.tar.gz’
V1.0.tar.gz [ <=> ] 20.80M 4.55MB/s in 4.4s
2021-01-29 11:44:39 (4.77 MB/s) - ‘V1.0.tar.gz’ saved [21815513]
[moldach@cedar1 TOOL_TMP_DIR]$ tar -zxvf V1.0.tar.gz
RUFUS-1.0/
RUFUS-1.0/.gitignore
RUFUS-1.0/CMakeLists.txt
RUFUS-1.0/Install.sh
RUFUS-1.0/Makefile
RUFUS-1.0/README.md
RUFUS-1.0/bin/
RUFUS-1.0/bin/AnnotateOverlap
RUFUS-1.0/bin/ConvertFASTqD.to.FASTQ
RUFUS-1.0/bin/ModelDist
RUFUS-1.0/bin/Overlap
RUFUS-1.0/bin/OverlapRegion
RUFUS-1.0/bin/RUFUS.Build
RUFUS-1.0/bin/RUFUS.Filter
RUFUS-1.0/bin/RUFUS.interpret
RUFUS-1.0/bin/ReplaceQwithDinFASTQD
RUFUS-1.0/bin/external/
RUFUS-1.0/bin/external/CMakeLists.txt
RUFUS-1.0/bin/externals/
RUFUS-1.0/bin/externals/.ignore
RUFUS-1.0/cloud/
RUFUS-1.0/cloud/CMakeLists.txt
RUFUS-1.0/cloud/CheckJellyHashList.sh
RUFUS-1.0/cloud/PassThroughSamCheck
RUFUS-1.0/cloud/PassThroughSamCheck.cpp
RUFUS-1.0/cloud/PassThroughSamCheck.stranded
RUFUS-1.0/cloud/PassThroughSamCheck.stranded.cpp
RUFUS-1.0/cloud/RUFUS.Filter.jellyPipe
RUFUS-1.0/cloud/RUFUS.Filter.jellyPipe.cpp
RUFUS-1.0/cloud/RUFUS.search.1kg
RUFUS-1.0/cloud/RUFUS.search.1kg.cpp
RUFUS-1.0/cloud/ReRunOverlap.asc.sh
RUFUS-1.0/cloud/RunJellyForRUFUS
RUFUS-1.0/cloud/RunJellyForRUFUS.UGP
RUFUS-1.0/cloud/RunRUFUS.1000G.withDupRemoce.sh
RUFUS-1.0/cloud/RunRUFUS.ASC.no1kg.sh
RUFUS-1.0/cloud/RunRUFUS.ASC.sh
RUFUS-1.0/cloud/RunRUFUS.Trio.sh
RUFUS-1.0/cloud/jellyfish-2.2.5.tar.gz
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.a
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.la
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.lai
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.so
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.so.2
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/.libs/libjellyfish-2.0.so.2.0.0
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/LICENSE
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/Makefile
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/Makefile.am
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/Makefile.in
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/README
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/aclocal.m4
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/compile
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.guess
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.h
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.h.in
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.log
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.status
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/config.sub
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/configure
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/configure.ac
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/depcomp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/doc/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/doc/jellyfish.man
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/doc/jellyfish.pdf
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/gtest.mk
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/allocators_mmap.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/atomic_bits_array.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/atomic_field.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/atomic_gcc.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/backtrace.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/binary_dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/bloom_common.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/bloom_counter2.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/bloom_filter.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/circular_buffer.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/compare_and_swap.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/cooperative_pool.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/cooperative_pool2.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/cpp_array.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/divisor.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/err.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/file_header.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/generator_manager.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/generic_file_header.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/hash_counter.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/int128.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/jellyfish.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/json.h
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/large_hash_array.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/large_hash_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/locks_pthread.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mapped_file.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_dna.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_dna_bloom_counter.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_heap.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_overlap_sequence_parser.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/mer_qual_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/misc.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/offsets_key_value.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/rectangular_binary_matrix.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/simple_circular_buffer.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/sorted_dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/stdio_filebuf.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/storage.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/stream_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/stream_manager.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/text_dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/thread_exec.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/time.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/token_ring.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish-2.2.5/jellyfish/whole_sequence_parser.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/allocators_mmap.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/atomic_bits_array.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/atomic_field.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/atomic_gcc.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/backtrace.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/binary_dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/bloom_common.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/bloom_counter2.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/bloom_filter.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/circular_buffer.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/compare_and_swap.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/cooperative_pool.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/cooperative_pool2.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/cpp_array.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/divisor.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/err.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/file_header.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/generator_manager.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/generic_file_header.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/hash_counter.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/int128.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/jellyfish.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/json.h
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/large_hash_array.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/large_hash_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/locks_pthread.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mapped_file.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_dna.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_dna_bloom_counter.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_heap.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_overlap_sequence_parser.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/mer_qual_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/misc.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/offsets_key_value.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/rectangular_binary_matrix.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/simple_circular_buffer.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/sorted_dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/stdio_filebuf.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/storage.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/stream_iterator.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/stream_manager.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/text_dumper.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/thread_exec.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/time.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/token_ring.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/include/jellyfish/whole_sequence_parser.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/install-sh
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish-2.0.pc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish-2.0.pc.in
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/.dirstamp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/backtrace.Po
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/bin_test_all-backtrace.Po
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/dbg.Po
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/generate_sequence.Po
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/merge_files.Po
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.deps/mersenne.Po
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/.dirstamp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/backtrace.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/dbg.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/dbg.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/fstream_default.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/generate_sequence.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/generate_sequence_cmdline.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/merge_files.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/merge_files.hpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/merge_files.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/mersenne.cpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/jellyfish/randomc.h
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/.dirstamp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/allocators_mmap.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/generator_manager.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/int128.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/jsoncpp.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/mer_dna.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/misc.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/rectangular_binary_matrix.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/storage.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/thread_exec.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.deps/time.Plo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.dirstamp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/allocators_mmap.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/generator_manager.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/int128.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/jsoncpp.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/mer_dna.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/misc.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/rectangular_binary_matrix.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/storage.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/thread_exec.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/.libs/time.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/allocators_mmap.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/allocators_mmap.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/allocators_mmap.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/generator_manager.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/generator_manager.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/generator_manager.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/int128.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/int128.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/int128.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/jsoncpp.cpp
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/jsoncpp.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/jsoncpp.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/libjellyfish-2.0.a
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/libjellyfish-2.0.la
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/libjellyfish-2.0.so
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/libjellyfish-2.0.so.2
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/libjellyfish-2.0.so.2.0.0
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/mer_dna.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/mer_dna.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/mer_dna.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/misc.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/misc.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/misc.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/pkgconfig/
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/pkgconfig/jellyfish-2.0.pc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/rectangular_binary_matrix.cc
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/rectangular_binary_matrix.lo
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/rectangular_binary_matrix.o
RUFUS-1.0/cloud/jellyfish-MODIFIED-merge/lib/storage.cc
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RUFUS-1.0/src/externals/fastahack/FastaHack.cpp
RUFUS-1.0/src/externals/fastahack/LargeFileSupport.h
RUFUS-1.0/src/externals/fastahack/Makefile
RUFUS-1.0/src/externals/fastahack/README
RUFUS-1.0/src/externals/fastahack/Region.h
RUFUS-1.0/src/externals/fastahack/disorder.c
RUFUS-1.0/src/externals/fastahack/disorder.h
RUFUS-1.0/src/externals/fastahack/libdisorder.LICENSE
RUFUS-1.0/src/externals/fastahack/split.cpp
RUFUS-1.0/src/externals/fastahack/split.h
RUFUS-1.0/src/externals/fastahack/tests/
RUFUS-1.0/src/externals/fastahack/tests/correct.fasta
RUFUS-1.0/src/externals/fastahack/tests/embedded_newline.fasta
RUFUS-1.0/src/externals/fastahack/tests/mismatched_lines.fasta
RUFUS-1.0/src/externals/fastahack/tests/trailing_newlines.fasta
RUFUS-1.0/src/externals/jellyfish-2.2.5.tar.gz
RUFUS-1.0/src/include/
RUFUS-1.0/src/include/Fasta.o
RUFUS-1.0/src/include/disorder.o
RUFUS-1.0/src/include/split.o
RUFUS-1.0/testRun/
RUFUS-1.0/testRun/clean.sh
RUFUS-1.0/testRun/runTest.sh
[moldach@cedar1 TOOL_TMP_DIR]$ cd RUFUS-1.0/
[moldach@cedar1 RUFUS-1.0]$ ll
total 53
drwxr-x--- 4 moldach moldach 4096 Sep 5 2018 bin
drwxr-x--- 3 moldach moldach 4096 Sep 5 2018 cloud
-rw-r----- 1 moldach moldach 381 Sep 5 2018 CMakeLists.txt
-rwxr-x--- 1 moldach moldach 3249 Sep 5 2018 configure.sh
drwxr-x--- 2 moldach moldach 4096 Sep 5 2018 externals
-rw-r----- 1 moldach moldach 4545 Sep 5 2018 Install.sh
-rw-r----- 1 moldach moldach 472 Sep 5 2018 Makefile
-rw-r----- 1 moldach moldach 5769 Sep 5 2018 README.md
drwxr-x--- 4 moldach moldach 4096 Sep 5 2018 resources
-rwxr-x--- 1 moldach moldach 20476 Sep 5 2018 runRufus.sh
drwxr-x--- 3 moldach moldach 4096 Sep 5 2018 scripts
drwxr-x--- 4 moldach moldach 4096 Sep 5 2018 src
drwxr-x--- 2 moldach moldach 4096 Sep 5 2018 testRun
[moldach@cedar1 RUFUS-1.0]$ nano README.md
Which version of gcc?
[moldach@cedar1 RUFUS-1.0]$ which gcc
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
Cmake with which gcc since it's not 4.9.2 (but is >)
[moldach@cedar1 RUFUS-1.0]$ cd bin/
[moldach@cedar1 bin]$ cmake ../ -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++)
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin
run make
[moldach@cedar1 bin]$ make
Scanning dependencies of target fastahack_project
[ 1%] Creating directories for 'fastahack_project'
[ 2%] Performing download step (git clone) for 'fastahack_project'
Cloning into 'fastahack_project'...
Checking out files: 100% (22/22), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
[ 4%] No patch step for 'fastahack_project'
[ 5%] No update step for 'fastahack_project'
[ 6%] Performing configure step for 'fastahack_project'
loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/fastahack/tmp/fastahack_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/fastahack/src/fastahack_project-build
[ 8%] Performing build step for 'fastahack_project'
Scanning dependencies of target fastahack_src_lib
[ 16%] Building C object src/CMakeFiles/fastahack_src_lib.dir/disorder.c.o
[ 33%] Building CXX object src/CMakeFiles/fastahack_src_lib.dir/Fasta.cpp.o
[ 50%] Building CXX object src/CMakeFiles/fastahack_src_lib.dir/split.cpp.o
[ 66%] Linking CXX static library libfastahack_src_lib.a
[ 66%] Built target fastahack_src_lib
Scanning dependencies of target fastahack
[ 83%] Building CXX object tools/CMakeFiles/fastahack.dir/FastaHack.cpp.o
[100%] Linking CXX executable fastahack
[100%] Built target fastahack
[ 9%] No install step for 'fastahack_project'
[ 10%] Completed 'fastahack_project'
[ 10%] Built target fastahack_project
Scanning dependencies of target bwa_project
[ 12%] Creating directories for 'bwa_project'
[ 13%] Performing download step (git clone) for 'bwa_project'
Cloning into 'bwa_project'...
Checking out files: 100% (77/77), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
[ 14%] No patch step for 'bwa_project'
[ 16%] No update step for 'bwa_project'
[ 17%] No configure step for 'bwa_project'
[ 18%] Performing build step for 'bwa_project'
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:879:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
bgint_t oldInverseSa0RelativeRank = 0;
^
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:953:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
unsigned int bitsInWordMinusBitPerChar;
^
ar: `u' modifier ignored since `D' is the default (see `U')
[ 20%] No install step for 'bwa_project'
[ 21%] Completed 'bwa_project'
[ 21%] Built target bwa_project
Scanning dependencies of target rufalu_project
[ 22%] Creating directories for 'rufalu_project'
[ 24%] Performing download step (git clone) for 'rufalu_project'
Cloning into 'rufalu_project'...
Checking out files: 100% (65/65), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
[ 25%] No patch step for 'rufalu_project'
[ 26%] No update step for 'rufalu_project'
[ 28%] Performing configure step for 'rufalu_project'
loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/tmp/rufalu_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
BAMTOOLS INCLUDE: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/include
BINARY_DIR: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project
SRC_DIR: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project
BAMTOOLS LIB DIR: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/include
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build
[ 29%] Performing build step for 'rufalu_project'
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[ 1%] Creating directories for 'zlib_project'
[ 3%] Performing download step (git clone) for 'zlib_project'
Cloning into 'zlib_project'...
Checking out files: 100% (254/254), done.
Note: checking out '50893291621658f355bc5b4d450a8d06a563053d'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b <new-branch-name>
HEAD is now at 5089329 zlib 1.2.8
[ 5%] No patch step for 'zlib_project'
[ 7%] No update step for 'zlib_project'
[ 9%] Performing configure step for 'zlib_project'
loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/tmp/zlib_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Renaming
-- /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/src/zlib_project/zconf.h
-- to 'zconf.h.included' because this file is included with zlib
-- but CMake generates it automatically in the build directory.
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/zlib/src/zlib_project-build
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Scanning dependencies of target zlib
[ 2%] Building C object CMakeFiles/zlib.dir/adler32.o
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Scanning dependencies of target minigzip
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[ 90%] Built target zlibstatic
Scanning dependencies of target example64
[ 92%] Building C object CMakeFiles/example64.dir/test/example.o
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[ 95%] Built target example64
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[ 97%] Building C object CMakeFiles/minigzip64.dir/test/minigzip.o
[100%] Linking C executable minigzip64
[100%] Built target minigzip64
[ 13%] No install step for 'zlib_project'
[ 15%] Completed 'zlib_project'
[ 15%] Built target zlib_project
Scanning dependencies of target bamtools_project
[ 17%] Creating directories for 'bamtools_project'
[ 19%] Performing download step (git clone) for 'bamtools_project'
Cloning into 'bamtools_project'...
Checking out files: 100% (184/184), done.
Note: checking out '45129fa9035847f54baa2c1750d4d3f526793e82'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b <new-branch-name>
HEAD is now at 45129fa Switched order of directory processing
[ 21%] No patch step for 'bamtools_project'
[ 23%] No update step for 'bamtools_project'
[ 25%] Performing configure step for 'bamtools_project'
loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/tmp/bamtools_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project-build
[ 26%] Performing build step for 'bamtools_project'
Scanning dependencies of target SharedHeaders
[ 0%] Built target SharedHeaders
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[ 1%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
[ 2%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
[ 3%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
[ 4%] Linking CXX static library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libjsoncpp.a
[ 4%] Built target jsoncpp
Scanning dependencies of target BamTools
[ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
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/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
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/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
^
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[ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
[ 42%] Linking CXX shared library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools.so
[ 42%] Built target BamTools
Scanning dependencies of target AlgorithmsHeaders
[ 42%] Built target AlgorithmsHeaders
Scanning dependencies of target BamTools-static
[ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
[ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
[ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
^
[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
[ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
^
[ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
[ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
[ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
[ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
[ 80%] Linking CXX static library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools.a
[ 80%] Built target BamTools-static
Scanning dependencies of target APIHeaders
[ 80%] Built target APIHeaders
Scanning dependencies of target BamTools-utils
[ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
[ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
[ 85%] Linking CXX static library /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/lib/libbamtools-utils.a
[ 85%] Built target BamTools-utils
Scanning dependencies of target bamtools_cmd
[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
[ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
[ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp: In member function ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:474:23: warning: typedef ‘TagElementType’ locally defined but not used [-Wunused-local-typedefs]
typedef T TagElementType;
^
In file included from /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamReader.h:14:0,
from /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:14:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = signed char; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = signed char]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:415:95: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
int elementLength = 0;
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = short int; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = short int]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:416:96: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = int]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:417:96: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = unsigned char; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = unsigned char]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:418:96: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = short unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = short unsigned int]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:419:97: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = unsigned int]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:420:97: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h: In instantiation of ‘bool BamTools::BamAlignment::GetTag(const string&, std::vector<T>&) const [with T = float; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:499:13: required from ‘bool BamTools::SplitTool::SplitToolPrivate::SplitListTagImpl(BamTools::BamAlignment&) [with T = float]’
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/toolkit/bamtools_split.cpp:421:94: required from here
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/src/api/BamAlignment.h:581:9: warning: variable ‘elementLength’ set but not used [-Wunused-but-set-variable]
[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
[100%] Linking CXX executable /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/bamtools/src/bamtools_project/bin/bamtools
[100%] Built target bamtools_cmd
[ 28%] No install step for 'bamtools_project'
[ 30%] Completed 'bamtools_project'
[ 30%] Built target bamtools_project
Scanning dependencies of target gtest_project
[ 32%] Creating directories for 'gtest_project'
[ 34%] Performing download step (git clone) for 'gtest_project'
Cloning into 'gtest_project'...
Checking out files: 100% (250/250), done.
Note: checking out '9ae086a9ebafabdc49b71bb7f3879f551adee09a'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b <new-branch-name>
HEAD is now at 9ae086a9 Merge pull request #874 from sejr/master
[ 36%] No patch step for 'gtest_project'
[ 38%] No update step for 'gtest_project'
[ 40%] Performing configure step for 'gtest_project'
loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/gtest/tmp/gtest_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/python (found version "2.7.13")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/gtest/src/gtest_project-build
[ 42%] Performing build step for 'gtest_project'
Scanning dependencies of target gmock_main
[ 9%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/__/googletest/src/gtest-all.cc.o
[ 18%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/src/gmock-all.cc.o
[ 27%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o
[ 36%] Linking CXX static library libgmock_main.a
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Scanning dependencies of target gmock
[ 45%] Building CXX object googlemock/CMakeFiles/gmock.dir/__/googletest/src/gtest-all.cc.o
[ 54%] Building CXX object googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o
[ 63%] Linking CXX static library libgmock.a
[ 63%] Built target gmock
Scanning dependencies of target gtest
[ 72%] Building CXX object googlemock/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
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Scanning dependencies of target gtest_main
[ 90%] Building CXX object googlemock/gtest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[100%] Linking CXX static library libgtest_main.a
[100%] Built target gtest_main
[ 44%] No install step for 'gtest_project'
[ 46%] Completed 'gtest_project'
[ 46%] Built target gtest_project
Scanning dependencies of target minimap2_project
[ 48%] Creating directories for 'minimap2_project'
[ 50%] Performing download step (git clone) for 'minimap2_project'
Cloning into 'minimap2_project'...
Checking out files: 100% (84/84), done.
Already on 'master'
Your branch is up to date with 'origin/master'.
Submodule 'lib/simde' (https://github.com/nemequ/simde.git) registered for path 'lib/simde'
Cloning into '/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project/lib/simde'...
Submodule path 'lib/simde': checked out 'b30129b3b48a6823013da2b309c50a081177b6b8'
Submodule 'munit' (https://github.com/nemequ/munit.git) registered for path 'lib/simde/test/munit'
Cloning into '/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/minimap2/src/minimap2_project/lib/simde/test/munit'...
Submodule path 'lib/simde/test/munit': checked out 'da8f73412998e4f1adf1100dc187533a51af77fd'
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format.c: In function ‘mm_write_sam3’:
format.c:395:36: warning: variable ‘this_rev’ set but not used [-Wunused-but-set-variable]
int this_rid = -1, this_pos = -1, this_rev = 0;
^
ar: `u' modifier ignored since `D' is the default (see `U')
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Scanning dependencies of target aludetect_external_project
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loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/aludetect_external_project-prefix/tmp/aludetect_external_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
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-- Detecting C compile features
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-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufalu/src/rufalu_project-build/externals/aludetect_external_project/bin
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Scanning dependencies of target aludetect_core
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Cloning into 'bedtools2_project'...
Checking out files: 100% (1065/1065), done.
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[ 40%] Performing build step for 'bedtools2_project'
Building BEDTools:
=========================================================
CXXFLAGS is [-g -Wall -O2 -std=c++11 ]
DETECTED_VERSION = v2.30.0-2-ga1be7683
CURRENT_VERSION =
Updating version file.
* compiling src/bedtools.cpp
* compiling src/annotateBed/annotateMain.cpp
* compiling src/annotateBed/annotateBed.cpp
* compiling src/bamToBed/bamToBed.cpp
src/bamToBed/bamToBed.cpp: In function ‘int bamtobed_main(int, char**)’:
src/bamToBed/bamToBed.cpp:88:10: warning: variable ‘useAlignmentScore’ set but not used [-Wunused-but-set-variable]
bool useAlignmentScore = false;
^
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/bamToBed/bamToBed.cpp:12:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/bamToFastq/bamToFastqMain.cpp
src/bamToFastq/bamToFastqMain.cpp: In function ‘int bamtofastq_main(int, char**)’:
src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable ‘haveFastq2’ set but not used [-Wunused-but-set-variable]
bool haveFastq2 = false;
^
* compiling src/bamToFastq/bamToFastq.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/bamToFastq/bamToFastq.h:15,
from src/bamToFastq/bamToFastq.cpp:15:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/bedToBam/bedToBam.cpp
src/bedToBam/bedToBam.cpp: In function ‘int bedtobam_main(int, char**)’:
src/bedToBam/bedToBam.cpp:60:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
bool haveMapQual = false;
^
* compiling src/bedpeToBam/bedpeToBam.cpp
src/bedpeToBam/bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’:
src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable]
bool haveMapQual = false;
^
* compiling src/bedToIgv/bedToIgv.cpp
* compiling src/bed12ToBed6/bed12ToBed6.cpp
* compiling src/closestFile/closestHelp.cpp
* compiling src/closestFile/closestFile.cpp
* compiling src/clusterBed/clusterMain.cpp
src/clusterBed/clusterMain.cpp: In function ‘int cluster_main(int, char**)’:
src/clusterBed/clusterMain.cpp:38:10: warning: variable ‘haveMaxDistance’ set but not used [-Wunused-but-set-variable]
bool haveMaxDistance = false;
^
* compiling src/clusterBed/clusterBed.cpp
* compiling src/complementFile/complementHelp.cpp
* compiling src/complementFile/complementFile.cpp
* compiling src/coverageFile/coverageHelp.cpp
* compiling src/coverageFile/coverageFile.cpp
* compiling src/expand/expand.cpp
* compiling src/fastaFromBed/fastaFromBedMain.cpp
* compiling src/fastaFromBed/fastaFromBed.cpp
* compiling src/flankBed/flankBedMain.cpp
* compiling src/flankBed/flankBed.cpp
* compiling src/genomeCoverageBed/genomeCoverageMain.cpp
* compiling src/genomeCoverageBed/genomeCoverageBed.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/utils/GenomeFile/NewGenomeFile.h:20,
from src/genomeCoverageBed/genomeCoverageBed.h:13,
from src/genomeCoverageBed/genomeCoverageBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/getOverlap/getOverlap.cpp
src/getOverlap/getOverlap.cpp: In function ‘int getoverlap_main(int, char**)’:
src/getOverlap/getOverlap.cpp:44:10: warning: variable ‘haveColumns’ set but not used [-Wunused-but-set-variable]
bool haveColumns = false;
^
* compiling src/groupBy/groupByHelp.cpp
* compiling src/groupBy/groupBy.cpp
* compiling src/intersectFile/intersectHelp.cpp
* compiling src/intersectFile/intersectFile.cpp
* compiling src/fisher/fisherHelp.cpp
* compiling src/fisher/fisher.cpp
* compiling src/fisher/kfunc.cpp
* compiling src/jaccard/jaccardHelp.cpp
* compiling src/jaccard/jaccard.cpp
* compiling src/linksBed/linksMain.cpp
* compiling src/linksBed/linksBed.cpp
* compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp
* compiling src/maskFastaFromBed/maskFastaFromBed.cpp
* compiling src/mapFile/mapHelp.cpp
* compiling src/mapFile/mapFile.cpp
* compiling src/mergeFile/mergeHelp.cpp
* compiling src/mergeFile/mergeFile.cpp
* compiling src/multiBamCov/multiBamCovMain.cpp
src/multiBamCov/multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’:
src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable]
bool haveBed = false;
^
src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable]
bool haveBams = false;
^
src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling src/multiBamCov/multiBamCov.cpp
In file included from src/utils/BamTools/include/BamReader.hpp:4:0,
from src/utils/BamTools/include/api/BamMultiReader.h:4,
from src/multiBamCov/multiBamCov.h:16,
from src/multiBamCov/multiBamCov.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/multiIntersectBed/multiIntersectBedMain.cpp
src/multiIntersectBed/multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’:
src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
bool haveFiles = false;
^
src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
bool haveGenome = false;
^
src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
bool haveFiller = true;
^
* compiling src/multiIntersectBed/multiIntersectBed.cpp
* compiling src/nucBed/nucBedMain.cpp
* compiling src/nucBed/nucBed.cpp
* compiling src/pairToBed/pairToBedMain.cpp
src/pairToBed/pairToBedMain.cpp: In function ‘int pairtobed_main(int, char**)’:
src/pairToBed/pairToBedMain.cpp:43:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling src/pairToBed/pairToBed.cpp
src/pairToBed/pairToBed.cpp: In member function ‘void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)’:
src/pairToBed/pairToBed.cpp:257:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
CHRPOS spanLength = 0;
^
src/pairToBed/pairToBed.cpp: In member function ‘bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)’:
src/pairToBed/pairToBed.cpp:310:12: warning: variable ‘spanLength’ set but not used [-Wunused-but-set-variable]
CHRPOS spanLength = 0;
^
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/pairToBed/pairToBed.h:15,
from src/pairToBed/pairToBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/pairToPair/pairToPairMain.cpp
src/pairToPair/pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’:
src/pairToPair/pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling src/pairToPair/pairToPair.cpp
src/pairToPair/pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’:
src/pairToPair/pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable]
bool found1 = false;
^
src/pairToPair/pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable]
bool found2 = false;
^
* compiling src/randomBed/randomBedMain.cpp
* compiling src/randomBed/randomBed.cpp
* compiling src/regressTest/regressTestMain.cpp
* compiling src/regressTest/RegressTest.cpp
* compiling src/reldist/reldistMain.cpp
* compiling src/reldist/reldist.cpp
src/reldist/reldist.cpp: In member function ‘void RelativeDistance::CalculateRelativeDistance()’:
src/reldist/reldist.cpp:129:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (low_idx != chrom_mids->size() - 1)
^
* compiling src/sampleFile/sampleHelp.cpp
* compiling src/sampleFile/sampleFile.cpp
* compiling src/shiftBed/shiftBedMain.cpp
* compiling src/shiftBed/shiftBed.cpp
* compiling src/shuffleBed/shuffleBedMain.cpp
* compiling src/shuffleBed/shuffleBed.cpp
* compiling src/slopBed/slopBedMain.cpp
* compiling src/slopBed/slopBed.cpp
* compiling src/sortBed/sortMain.cpp
* compiling src/sortBed/sortBed.cpp
* compiling src/spacingFile/spacingHelp.cpp
* compiling src/spacingFile/spacingFile.cpp
* compiling src/split/splitBedMain.cpp
* compiling src/split/splitBed.cpp
* compiling src/subtractFile/subtractHelp.cpp
* compiling src/subtractFile/subtractFile.cpp
* compiling src/summaryFile/summaryHelp.cpp
* compiling src/summaryFile/summaryFile.cpp
* compiling src/tagBam/tagBamMain.cpp
* compiling src/tagBam/tagBam.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/tagBam/tagBam.h:17,
from src/tagBam/tagBam.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/unionBedGraphs/unionBedGraphsMain.cpp
src/unionBedGraphs/unionBedGraphsMain.cpp: In function ‘int unionbedgraphs_main(int, char**)’:
src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable]
bool haveFiles = false;
^
src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable]
bool haveGenome = false;
^
src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable]
bool haveFiller = true;
^
* compiling src/unionBedGraphs/unionBedGraphs.cpp
* compiling src/windowBed/windowMain.cpp
* compiling src/windowBed/windowBed.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/windowBed/windowBed.h:15,
from src/windowBed/windowBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/windowMaker/windowMakerMain.cpp
* compiling src/windowMaker/windowMaker.cpp
* compiling src/utils/FileRecordTools/FileRecordMgr.cpp
* compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp
* compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp
* compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
* compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
* compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function ‘bool BufferedStreamMgr::readFileChunk()’:
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_mainBufCurrLen < _useBufSize) {
^
* compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1:0,
from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14,
from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8:
src/utils/BamTools/include/SamHeader.hpp: In function ‘int htslib_future::sam_hdr_rebuild(bam_hdr_t*)’:
src/utils/BamTools/include/SamHeader.hpp:32:25: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
* compiling src/utils/FileRecordTools/Records/Record.cpp
* compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp
* compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp
* compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp
* compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp
* compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp
* compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp
* compiling src/utils/FileRecordTools/Records/PlusFields.cpp
* compiling src/utils/FileRecordTools/Records/GffRecord.cpp
* compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp
* compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
* compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp
* compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp
* compiling src/utils/FileRecordTools/Records/BamRecord.cpp
* compiling src/utils/FileRecordTools/Records/VcfRecord.cpp
* compiling src/utils/FileRecordTools/Records/BlockMgr.cpp
src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function ‘int BlockMgr::getNonRedundantOverlap()’:
src/utils/FileRecordTools/Records/BlockMgr.cpp:194:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 1; i < _overlapStarts.size(); ++i)
^
* compiling src/utils/FileRecordTools/Records/StrandQueue.cpp
* compiling src/utils/FileRecordTools/Records/RecordMgr.cpp
* compiling src/utils/FileRecordTools/Records/RecordList.cpp
* compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp
* compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp
* compiling src/utils/bedFile/bedFile.cpp
* compiling src/utils/BinTree/BinTree.cpp
* compiling src/utils/version/version.cpp
* compiling src/utils/bedGraphFile/bedGraphFile.cpp
* compiling src/utils/chromsweep/chromsweep.cpp
* compiling src/utils/Contexts/ContextBase.cpp
* compiling src/utils/Contexts/ContextIntersect.cpp
* compiling src/utils/Contexts/ContextFisher.cpp
* compiling src/utils/Contexts/ContextMap.cpp
* compiling src/utils/Contexts/ContextSample.cpp
* compiling src/utils/Contexts/ContextSpacing.cpp
* compiling src/utils/Contexts/ContextMerge.cpp
* compiling src/utils/Contexts/ContextJaccard.cpp
* compiling src/utils/Contexts/ContextClosest.cpp
* compiling src/utils/Contexts/ContextSubtract.cpp
* compiling src/utils/Contexts/ContextCoverage.cpp
* compiling src/utils/Contexts/ContextComplement.cpp
* compiling src/utils/Contexts/ContextGroupBy.cpp
* compiling src/utils/Contexts/ContextSummary.cpp
* compiling src/utils/general/ParseTools.cpp
* compiling src/utils/general/PushBackStreamBuf.cpp
* compiling src/utils/general/CompressionTools.cpp
* compiling src/utils/general/Tokenizer.cpp
* compiling src/utils/general/CommonHelp.cpp
* compiling src/utils/general/ErrorMsg.cpp
* compiling src/utils/general/Random.cpp
* compiling src/utils/fileType/fileType.cpp
* compiling src/utils/fileType/FileRecordTypeChecker.cpp
src/utils/fileType/FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’:
src/utils/fileType/FileRecordTypeChecker.cpp:366:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < len; j++) {
^
* compiling src/utils/bedFilePE/bedFilePE.cpp
* compiling src/utils/KeyListOps/KeyListOps.cpp
* compiling src/utils/KeyListOps/KeyListOpsMethods.cpp
* compiling src/utils/NewChromsweep/NewChromsweep.cpp
* compiling src/utils/NewChromsweep/CloseSweep.cpp
* compiling src/utils/sequenceUtilities/sequenceUtils.cpp
* compiling src/utils/tabFile/tabFile.cpp
* compiling src/utils/BamTools-Ancillary/BamAncillary.cpp
* compiling src/utils/BlockedIntervals/BlockedIntervals.cpp
* compiling src/utils/Fasta/Fasta.cpp
* compiling src/utils/Fasta/split.cpp
* compiling src/utils/VectorOps/VectorOps.cpp
* compiling src/utils/GenomeFile/NewGenomeFile.cpp
* compiling src/utils/GenomeFile/GenomeFile.cpp
src/utils/GenomeFile/GenomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
long c2;
^
* compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector<long int>*)’:
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (context->getNumClosestHitsWanted() > keyList.size())
^
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function ‘void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)’:
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:455:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < _context->getNumInputFiles(); i++)
^
* compiling src/utils/ToolBase/ToolBase.cpp
* compiling src/utils/driver/BedtoolsDriver.cpp
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
* compiling src/htsutil.cpp
[ 41%] No install step for 'bedtools2_project'
[ 42%] Completed 'bedtools2_project'
[ 42%] Built target bedtools2_project
Scanning dependencies of target rufus_external_project
[ 44%] Creating directories for 'rufus_external_project'
[ 45%] No download step for 'rufus_external_project'
[ 46%] No patch step for 'rufus_external_project'
[ 48%] No update step for 'rufus_external_project'
[ 49%] Performing configure step for 'rufus_external_project'
loading initial cache file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufus_external_project-prefix/tmp/rufus_external_project-cache-.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/bin/externals/rufus_external_project/bin
[ 50%] Performing build step for 'rufus_external_project'
[ 52%] No install step for 'rufus_external_project'
[ 53%] Completed 'rufus_external_project'
[ 53%] Built target rufus_external_project
Scanning dependencies of target rufus_util
[ 54%] Building CXX object src/CMakeFiles/rufus_util.dir/Util.cpp.o
[ 56%] Linking CXX static library librufus_util.a
[ 56%] Built target rufus_util
Scanning dependencies of target RUFUS.interpret
[ 57%] Building CXX object src/CMakeFiles/RUFUS.interpret.dir/RUFUS.interpret.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/RUFUS.interpret.cpp:3128:3: warning: backslash and newline separated by space
\n\
^
[ 58%] Linking CXX executable ../RUFUS.interpret
[ 58%] Built target RUFUS.interpret
Scanning dependencies of target OverlapSam
[ 60%] Building CXX object src/CMakeFiles/OverlapSam.dir/OverlapSam.cpp.o
[ 61%] Linking CXX executable ../OverlapSam
[ 61%] Built target OverlapSam
Scanning dependencies of target AnnotateOverlap
[ 62%] Building CXX object src/CMakeFiles/AnnotateOverlap.dir/AnnotateOverlap.cpp.o
[ 64%] Linking CXX executable ../AnnotateOverlap
[ 64%] Built target AnnotateOverlap
Scanning dependencies of target RUFUS.Build
[ 65%] Building CXX object src/CMakeFiles/RUFUS.Build.dir/RUFUS.Build.cpp.o
[ 66%] Linking CXX executable ../RUFUS.Build
[ 66%] Built target RUFUS.Build
Scanning dependencies of target rufus_core
[ 68%] Building CXX object src/CMakeFiles/rufus_core.dir/Util.cpp.o
[ 69%] Building CXX object src/CMakeFiles/rufus_core.dir/AnnotateOverlap.cpp.o
[ 70%] Building CXX object src/CMakeFiles/rufus_core.dir/ConvertFASTqD.to.FASTQ.cpp.o
[ 72%] Building CXX object src/CMakeFiles/rufus_core.dir/ModelDist.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp: In function ‘int main(int, char**)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:701:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:700:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:625:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:624:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:590:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:589:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:558:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:557:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
[ 73%] Building CXX object src/CMakeFiles/rufus_core.dir/Overlap.cpp.o
[ 74%] Building CXX object src/CMakeFiles/rufus_core.dir/OverlapRegion.cpp.o
[ 76%] Building CXX object src/CMakeFiles/rufus_core.dir/OverlapSam.cpp.o
[ 77%] Building CXX object src/CMakeFiles/rufus_core.dir/ReplaceQwithDinFASTQD.cpp.o
[ 78%] Building CXX object src/CMakeFiles/rufus_core.dir/RUFUS.Filter.cpp.o
[ 80%] Building CXX object src/CMakeFiles/rufus_core.dir/RUFUS.Build.cpp.o
[ 81%] Building CXX object src/CMakeFiles/rufus_core.dir/RUFUS.interpret.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/RUFUS.interpret.cpp:3128:3: warning: backslash and newline separated by space
\n\
^
[ 82%] Building CXX object src/CMakeFiles/rufus_core.dir/RUFUS.1kg.filter.cpp.o
[ 84%] Linking CXX static library librufus_core.a
[ 84%] Built target rufus_core
Scanning dependencies of target ModelDist
[ 85%] Building CXX object src/CMakeFiles/ModelDist.dir/ModelDist.cpp.o
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp: In function ‘int main(int, char**)’:
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:701:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:700:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:625:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:624:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:590:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:589:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:558:21: warning: iteration 8u invokes undefined behavior [-Waggressive-loop-optimizations]
if (values[x] < lowest) {
^
/scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/src/ModelDist.cpp:557:25: note: containing loop
for (int x = 1; x <= 10; x++) {
^
[ 86%] Linking CXX executable ../ModelDist
[ 86%] Built target ModelDist
Scanning dependencies of target OverlapRegion
[ 88%] Building CXX object src/CMakeFiles/OverlapRegion.dir/OverlapRegion.cpp.o
[ 89%] Linking CXX executable ../OverlapRegion
[ 89%] Built target OverlapRegion
Scanning dependencies of target RUFUS.Filter
[ 90%] Building CXX object src/CMakeFiles/RUFUS.Filter.dir/RUFUS.Filter.cpp.o
[ 92%] Linking CXX executable ../RUFUS.Filter
[ 92%] Built target RUFUS.Filter
Scanning dependencies of target ReplaceQwithDinFASTQD
[ 93%] Building CXX object src/CMakeFiles/ReplaceQwithDinFASTQD.dir/ReplaceQwithDinFASTQD.cpp.o
[ 94%] Linking CXX executable ../ReplaceQwithDinFASTQD
[ 94%] Built target ReplaceQwithDinFASTQD
Scanning dependencies of target ConvertFASTqD.to.FASTQ
[ 96%] Building CXX object src/CMakeFiles/ConvertFASTqD.to.FASTQ.dir/ConvertFASTqD.to.FASTQ.cpp.o
[ 97%] Linking CXX executable ../ConvertFASTqD.to.FASTQ
[ 97%] Built target ConvertFASTqD.to.FASTQ
Scanning dependencies of target Overlap
[ 98%] Building CXX object src/CMakeFiles/Overlap.dir/Overlap.cpp.o
[100%] Linking CXX executable ../Overlap
[100%] Built target Overlap
Try to run bash runTest.sh
[moldach@cedar1 bin]$ cd ../testRun/
[moldach@cedar1 testRun]$ salloc --time=0:20:0 --mem=5000
salloc: Pending job allocation 60732837
salloc: job 60732837 queued and waiting for resources
salloc: job 60732837 has been allocated resources
salloc: Granted job allocation 60732837
[moldach@cdr767 testRun]$ bash runTest.sh
arg ref without fa is /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/references/small_test_human_reference_v37_decoys
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Final reference path being used is /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
Final bwa reference path being used is /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
proband extension is bam
you provided the proband bam file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/testData/Child.bam
parent file name is Mother.bam
parent file extension name is bam
You provided the control bam file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/testData/Mother.bam
parent file name is Father.bam
parent file extension name is bam
You provided the control bam file /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/testData/Father.bam
~~~~~~~~~~~~ printing out paramater values used in script ~~~~~~~~~~~~~~~~
value of ProbandGenerator Child.bam.generator
Value of ParentGenerators:
Mother.bam.generator
Father.bam.generator
Value of K is: 25
Value of Threads is: 40
value of ref is: /scratch/moldach/TOOL_TMP_DIR/RUFUS-1.0/testRun/../resources/references/small_test_human_reference_v37_decoys.fa
value of min is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Did not provide refHash
$_arg_min is NOT empty
_arg_min is 8
MutantMinCov is 8
Building parentString...
parent is Mother.bam.generator
parents string equals Mother.bam.generator.Jhash
parent is Father.bam.generator
parents string equals Mother.bam.generator.Jhash Father.bam.generator.Jhash
./../runRufus.sh: line 469: /usr/bin/time: No such file or directory
./../runRufus.sh: line 469: /usr/bin/time: No such file or directory
./../runRufus.sh: line 472: /usr/bin/time: No such file or directory
@@@@@@@@@@@__WARNING__@@@@@@@@@@@@@
Mother.bam.generator.Jhash is empty
Killing run with exit status 1
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
runTest.sh: line 1: 7645 Killed ./../runRufus.sh -s $PWD/../resources/testData/Child.bam -c $PWD/../resources/testData/Mother.bam $PWD/../resources/testData/Father.bam -k 25 -t 40 -m 8 -r $PWD/../resources/references/small_test_human_reference_v37_decoys.fa
