Problem running make
Tj-Idowu opened this issue · 2 comments
When I run make I get this error:
`user@servername:~/mccortex$ make all
cd libs && make core
make[1]: Entering directory '/home/ambarnilg/mccortex/libs'
Run configure if config makefile not created
cd htslib && ( if ! [ -f config.mk ]; then autoreconf && ./configure --disable-lzma --disable-bz2 --disable-libcurl; fi; make -e )
/bin/bash: autoreconf: command not found
make[2]: Entering directory '/home/ambarnilg/mccortex/libs/htslib'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/ambarnilg/mccortex/libs/htslib'
cd string_buffer && make all
make[2]: Entering directory '/home/ambarnilg/mccortex/libs/string_buffer'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/ambarnilg/mccortex/libs/string_buffer'
cd bit_array && make all
make[2]: Entering directory '/home/ambarnilg/mccortex/libs/bit_array'
cd dev && make
make[3]: Entering directory '/home/ambarnilg/mccortex/libs/bit_array/dev'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/ambarnilg/mccortex/libs/bit_array/dev'
cd examples && make
make[3]: Entering directory '/home/ambarnilg/mccortex/libs/bit_array/examples'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/ambarnilg/mccortex/libs/bit_array/examples'
make[2]: Leaving directory '/home/ambarnilg/mccortex/libs/bit_array'
cd seq_file && make HTSLIB=../htslib all
make[2]: Entering directory '/home/ambarnilg/mccortex/libs/seq_file'
mkdir -p bin
cc -Wall -Wextra -std=c99 -pedantic -I. -O3 -o bin/dnacat tools/dna_cat.c -I ../htslib -D_USESAM=1 ../htslib/libhts.a -lm -lpthread -lz -lm
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33:0,
from /usr/include/stdlib.h:25,
from tools/dna_cat.c:11:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from ./seq_file.h:27:0,
from tools/dna_cat.c:23:
../htslib/htslib/hfile.h: In function ‘hwrite’:
../htslib/htslib/hfile.h:261:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (fp->limit - fp->begin < nbytes){
^
../htslib/libhts.a(cram_io.o): In function lzma_mem_deflate': /home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:678: undefined reference to lzma_stream_buffer_bound'
/home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:684: undefined reference to lzma_easy_buffer_encode' ../htslib/libhts.a(cram_io.o): In function cram_compress_by_method':
/home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:1040: undefined reference to BZ2_bzBuffToBuffCompress' ../htslib/libhts.a(cram_io.o): In function cram_uncompress_block':
/home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:966: undefined reference to BZ2_bzBuffToBuffDecompress' ../htslib/libhts.a(cram_io.o): In function lzma_mem_inflate':
/home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:700: undefined reference to lzma_easy_decoder_memusage' /home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:700: undefined reference to lzma_stream_decoder'
/home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:715: undefined reference to lzma_code' /home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:728: undefined reference to lzma_code'
/home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:737: undefined reference to lzma_end' collect2: error: ld returned 1 exit status Makefile:32: recipe for target 'bin/dnacat' failed make[2]: *** [bin/dnacat] Error 1 make[2]: Leaving directory '/home/ambarnilg/mccortex/libs/seq_file' Makefile:49: recipe for target 'seq_file' failed make[1]: *** [seq_file] Error 2 make[1]: Leaving directory '/home/ambarnilg/mccortex/libs' Makefile:238: recipe for target 'libs-core' failed make: *** [libs-core] Error 2
I tried running apt install -y r-base-core but that is also not working.
It looks like autoreconf is not installed. Here are some instructions https://askubuntu.com/questions/265471/autoreconf-not-found-error-during-making-qemu-1-4-0/490839
I've installed autoreconf but I've come across a different problem.
$ ./mccortex/bin/mccortex31 build -m 8G -k 31 --sample FCH3MMVBBXX-wHAXPI027380-76_L1 --seq2 Clean_Reads/FCH3MMVBBXX-wHAXPI027380-76_L1_1.fq:Clean_Reads/FCH3MMVBBXX-wHAXPI027380-76_L1_2.fq External/Out/FCH3MMVBBXX-wHAXPI027380-76_L1.ctx [29 Aug 2019 10:14:31-BuP][cmd] ./mccortex/bin/mccortex31 build -m 8G -k 31 --sample FCH3MMVBBXX-wHAXPI027380-76_L1 --seq2 Clean_Reads/FCH3MMVBBXX-wHAXPI027380-76_L1_1.fq:Clean_Reads/FCH3MMVBBXX-wHAXPI027380-76_L1_2.fq External/Out/FCH3MMVBBXX-wHAXPI027380-76_L1.ctx
[29 Aug 2019 10:14:31-BuP][cwd] /home/tj/Infant_Metagenomic_Data
[29 Aug 2019 10:14:31-BuP][version] mccortex=heads/master zlib=1.2.11 htslib=1.9-66-gbcf9bff-dirty ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31
[29 Aug 2019 10:14:31-BuP] Saving graph to: External/Out/FCH3MMVBBXX-wHAXPI027380-76_L1.ctx
[29 Aug 2019 10:14:31-BuP][sample] 0: FCH3MMVBBXX-wHAXPI027380-76_L1
[29 Aug 2019 10:14:31-BuP][task] Clean_Reads/FCH3MMVBBXX-wHAXPI027380-76_L1_1.fq; FASTQ offset: auto-detect, threshold: off; cut homopolymers: off; remove PCR duplicates: no; colour: 0
[29 Aug 2019 10:14:31-BuP][task] Clean_Reads/FCH3MMVBBXX-wHAXPI027380-76_L1_2.fq; FASTQ offset: auto-detect, threshold: off; cut homopolymers: off; remove PCR duplicates: no; colour: 0
[29 Aug 2019 10:14:31-BuP][memory] 104 bits per kmer
[29 Aug 2019 10:14:31-BuP][memory] graph: 8GB
[29 Aug 2019 10:14:31-BuP][cmd_mem.c:147] Fatal Error: Requesting more memory than is available [ Reqeusted: -m 8GB RAM: 7.7GB ]
I tried increasing the memory but it keeps requesting an increase. The data I'm working with should not require more than 8GB.