installation issue (fatal errors & warnings)

[sjfleck]

Hi, I'm new to using MaSuRCA and I'm having difficulties with the installation. I followed the directions on your page and ended up with many errors running "./install.sh". In general, here's an example of a "fatal error":

swig/perl5/swig_wrap.cpp:743:10: fatal error: EXTERN.h: No such file or directory

include "EXTERN.h"

      ^~~~~~~~~~

compilation terminated.

Here's a long list of all the instances of "fatal error": Line 200: swig/perl5/swig_wrap.cpp:743:10: fatal error: EXTERN.h: No such file or directory Line 391: src/error_correct_reads.cc:25:10: fatal error: jellyfish/atomic_gcc.hpp: No such file or directory Line 397: src/merge_mate_pairs.cc:4:10: fatal error: jellyfish/stream_manager.hpp: No such file or directory Line 402: src/create_database.cc:23:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 451: src2/findMatchesBetweenKUnitigsAndReads.cc:31:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 457: src2/createKUnitigMaxOverlaps.cc:65:10: fatal error: jellyfish/err.hpp: No such file or directory Line 462: src/bloom_query.cc:2:10: fatal error: jellyfish/mapped_file.hpp: No such file or directory Line 467: src/rename_filter_fastq.cc:21:10: fatal error: jellyfish/err.hpp: No such file or directory Line 472: src/filter_overlap_file.cc:23:10: fatal error: jellyfish/jellyfish.hpp: No such file or directory Line 477: src/error_corrected2frg.cc:24:10: fatal error: jellyfish/err.hpp: No such file or directory Line 485: ./include/jflib/pool.hpp:22:10: fatal error: jellyfish/circular_buffer.hpp: No such file or directory Line 490: src/create_k_unitigs_large_k2.cc:24:10: fatal error: jellyfish/jellyfish.hpp: No such file or directory Line 496: ./src/create_k_unitigs_common.hpp:21:10: fatal error: jellyfish/thread_exec.hpp: No such file or directory Line 501: src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.cc:27:10: fatal error: jellyfish/err.hpp: No such file or directory Line 505: src2/getSuperReadInsertCountsFromReadPlacementFile.cc:27:10: fatal error: jellyfish/err.hpp: No such file or directory Line 511: src2/runByDirectory.cc:20:10: fatal error: jellyfish/err.hpp: No such file or directory Line 516: src2/joinKUnitigs_v3.cc:48:10: fatal error: jellyfish/err.hpp: No such file or directory Line 521: src2/collectReadSequencesForLocalGapClosing.cc:19:10: fatal error: jellyfish/err.hpp: No such file or directory Line 525: src/sorted_merge.cc:29:10: fatal error: jellyfish/err.hpp: No such file or directory Line 920: ./src_jf_aligner/superread_parser.hpp:8:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 927: ./src_jf_aligner/superread_parser.hpp:8:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 933: ./src_jf_aligner/superread_parser.hpp:8:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 940: ./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 948: ./include/jflib/pool.hpp:22:10: fatal error: jellyfish/circular_buffer.hpp: No such file or directory Line 956: ./include/jflib/pool.hpp:22:10: fatal error: jellyfish/circular_buffer.hpp: No such file or directory Line 963: ./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 971: ./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 975: ./src_jf_aligner/output_file.hpp:9:10: fatal error: jellyfish/err.hpp: No such file or directory Line 984: ./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory Line 1031: swig/perl5/swig_wrap.cpp:743:10: fatal error: EXTERN.h: No such file or directory

Additionally, I'm getting many warnings. There are even more warnings than "fatal errors" so I won't list them all. Here are a couple:

standardPregraph/contig.c:79:2: warning: implicit declaration of function ‘sortedge’; did you mean ‘loadEdge’? [-Wimplicit-function-declaration] sortedge(); ^~~~ loadEdge

standardPregraph/cutTip_graph2.c:231:2: warning: implicit declaration of function ‘linearConcatenate2’; did you mean ‘linearConcatenate’? [-Wimplicit-function-declaration] linearConcatenate2 ( last ); ^~~~~~ linearConcatenate

I'm hoping that you could help me understand why I'm getting all there errors. I will attach a text file with the entire install log as well if you're interested. Thank you, Steve

MaSuRCA_install.txt

[LisaBlazek]

how did you solve it? i currently have the same issue

[jgorz]

I am also having the same issue. Have you had any luck installing?

[dantefff]

It seems that the problem is compiling Jellyfish. I think this is solved by my pull request: #225

[sjfleck]

I'm sure I'm too late to help anyone, but I can show how I ultimately installed the program In Dec, 2020. I didn't actually need to assemble my genomes using MaSuRCA back in Jan, 2020. I was just doing it for fun (and failing). Nearly a year later, I actually needed to do ~20 MaSuRCA assemblies and I successfully installed and assembled the genomes using MaSuRCA-3.2.7 and MaSuRCA-3.4.3 (later renamed MaSuRCA-4.0.0 because of how much faster it was).

I should note that I ran MaSuRCA on my university's cluster that uses the Slurm workload manager. Additionally, we load programs using the Lua module system. Here are the few steps I used to install MaSuRCA-3.4.3:

download MaSuRCA-3.4.3.tar.gz from https://github.com/alekseyzimin/masurca

transfer it to my personal modulefiles directory

cd /full/path/to/modulefiles tar -zxvf MaSuRCA-3.4.3.tar.gz cd MaSuRCA-3.4.3 module load gcc/10.2.0 #automatically available by our university module use -a /full/path/to/modulefiles/Allluas #this is my personal directory with my .lua files module load perl-5.32.0 #installed previously ./install.sh

And here is how I load MaSuRCA in a script that I submit to our cluster:

module load gcc/10.2.0 module use -a /full/path/to/modulefiles/Allluas module load perl-5.32.0 module load MaSuRCA-3.4.3

[buhanfeng]

Thx @sjfleck for his sharing. But seems it only works on cluster? I'm not sure about it. Anyway, here is a more staightforward solution, running 'yum install perl-ExtUtils-Embed' in Centos or apt in Ubuntu and so on.

[sjfleck]

@buhanfeng that's right. My solution should only work in specific circumstances. I wanted to share incase other people needed to install on a platform where they don't have admin permissions. Thanks for sharing your solution as well!

[V-JJ]

Hello @dantefff !

We have the same problem when trying to compile masurca. Could you explain how can we use the solution that you have proposed? We are newbies with git...

Thanks in advance,

[dantefff]

Hello @V-JJ

If you don't want to mess with git, you can see my small change here: https://github.com/alekseyzimin/masurca/pull/225/files and you can apply it manually in the code cloned from this repository.

[dantefff]

Anyway, im taking a look and it seems that developers have addressed the issue in the current code base. @V-JJ which version are you trying to compile?

[V-JJ]

Hello!

I tried to install the latest version MaSuRCA 4.1.0 . Today, I am going to try the small change code change that you've mentioned above.

Thanks for the fast reply!