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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
113 stars 25 forks source link

Problem running make #86

Open Tj-Idowu opened 5 years ago

Tj-Idowu commented 5 years ago

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 tolzma_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 functioncram_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 functioncram_uncompress_block': /home/ambarnilg/mccortex/libs/htslib/cram/cram_io.c:966: undefined reference to BZ2_bzBuffToBuffDecompress' ../htslib/libhts.a(cram_io.o): In functionlzma_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 tolzma_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 tolzma_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.

winni2k commented 5 years ago

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

Tj-Idowu commented 5 years ago

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.