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alekseyzimin / masurca

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Error in assemble.sh #6

Closed milw closed 6 years ago

milw commented 6 years ago

masurca 3.2.5 writes 'CA8/Linux-amd64/bin' in assemble.sh for starting the CA run, but the install path is actually just 'CA/Linux-amd64/bin' this is the error: [Mon Mar 5 09:45:54 CST 2018] Using linking mates Using CABOG from is /media/data/software/MaSuRCA-3.2.5/bin/../CA8/Linux-amd64/bin runCA not found at /media/data/software/MaSuRCA-3.2.5/bin/../CA8/Linux-amd64/bin! cat: CA_dir.txt: No such file or directory [Mon Mar 5 09:45:54 CST 2018] Assembly stopped or failed, see .log

alekseyzimin commented 6 years ago

Sorry, not correct, both paths are valid. CA/Linux-amd64/bin is CA version 6 and CA8/Linux-amd64/bin is version 8. Version 6 works better for Illumina-only data and version 8 workd folr long-read assemblies (nanopore/pacbio). Please do not use 3.2.5, it is not ready yet for public use.

milw commented 6 years ago

OK, I deleted 3.2.5 and am trying to install 3.2.4 from tarball. Make hits an error:make[1]: Entering directory '/media/data/software/MaSuRCA-3.2.4/global-1/CA8' CXXLD bin/meryl CXXLD bin/overmerry CXXLD bin/merTrim CXXLD bin/buildUnitigs CXXLD bin/bogart CXXLD bin/bogus CXXLD bin/bogusness CXXLD bin/analyzePosMap CXXLD bin/metagenomics_ovl_analyses CXXLD bin/asmOutputStatistics CXXLD bin/computeCoverageStat CXXLD bin/chimChe CXXLD bin/buildRefContigs CXXLD bin/greedyFragmentTiling lib/libseq.a(seqStore.o): In functionmemset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference to __warn_memset_zero_len' collect2: error: ld returned 1 exit status

alekseyzimin commented 6 years ago

What is your gcc version?

milw commented 6 years ago

4.9.3 I am trying switching back to gcc/g++ 4.7 Nope, 4.7.4 gives same error as above, ` CXXLD bin/greedyFragmentTiling lib/libseq.a(seqStore.o): In functionmemset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference to __warn_memset_zero_len' collect2: error: ld returned 1 exit status Makefile:3344: recipe for target 'bin/meryl' failed make[1]: *** [bin/meryl] Error 1 make[1]: *** Waiting for unfinished jobs.... lib/libseq.a(seqStore.o): In functionmemset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference to __warn_memset_zero_len' collect2: error: ld returned 1 exit status Makefile:3453: recipe for target 'bin/overmerry' failed make[1]: *** [bin/overmerry] Error 1 src/AS_MER/merTrim.o: In functionmemset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference to __warn_memset_zero_len' /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference towarn_memset_zero_len' lib/libseq.a(seqStore.o): In function memset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference towarn_memset_zero_len' collect2: error: ld returned 1 exit status Makefile:3324: recipe for target 'bin/merTrim' failed make[1]: [bin/merTrim] Error 1 make[1]: Leaving directory '/media/data/software/MaSuRCA-3.2.3/global-1/CA8' Makefile:847: recipe for target 'install-special' failed make: [install-special] Error 2'

milw commented 6 years ago

As of Mar 22 2018, the 3.2.4 source downloaded from the ftp site has installed correctly, I now have both CA and CA8 in the installation.

farihakomel commented 4 years ago

I am having similar issue with MaSuRCA 3.3.4 assembler :

lib/libseq.a(seqStore.o): In function memset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference to__warn_memset_zero_len' collect2: error: ld returned 1 exit status Makefile:3344: recipe for target 'bin/meryl' failed make[1]: [bin/meryl] Error 1 make[1]: Waiting for unfinished jobs.... src/AS_MER/merTrim.o: In function memset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference towarn_memset_zero_len' /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference to `warn_memset_zero_len' lib/libseq.a(seqStore.o): In function memset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference towarn_memset_zero_len' collect2: error: ld returned 1 exit status Makefile:3324: recipe for target 'bin/merTrim' failed make[1]: *** [bin/merTrim] Error 1 lib/libseq.a(seqStore.o): In function memset': /usr/include/x86_64-linux-gnu/bits/string3.h:86: undefined reference towarn_memset_zero_len' collect2: error: ld returned 1 exit status Makefile:3453: recipe for target 'bin/overmerry' failed make[1]: [bin/overmerry] Error 1 make[1]: Leaving directory '/home/nadia/Downloads/MaSuRCA-3.3.4/global-1/CA8' Makefile:847: recipe for target 'install-special' failed make: [install-special] Error 2

any solutions?