How to compile Multiz

Question

[Santex]

I am currently trying to run Multiz locally and visualize the results on the UCSC Genome Browser. I have completed the Lastz, chaining, and netting steps, and am now at the Multiz stage. However, I am encountering difficulties downloading and compiling Multiz. Please help me out with it.

Here is the error it returns to me.

(base):~$ git clone https://github.com/multiz/multiz.git
Cloning into 'multiz'...
remote: Enumerating objects: 103, done.
remote: Total 103 (delta 0), reused 0 (delta 0), pack-reused 103 (from 1)
Receiving objects: 100% (103/103), 499.20 KiB | 1.55 MiB/s, done.
Resolving deltas: 100% (37/37), done.
(base):~$ ls
Documents  HiCExplorer   kent           lastz-distrib  multiz
Downloads  genofig-main  lastz-1.04.22  miniconda3

(base):~$ cd multiz

(base):~/multiz$ ls
LICENSE          charvec.h               maf_order.h           multiz.c      single_cov2.c
Makefile         dna_nib.c               maf_order_main.c      mz_preyama.c  speciesTree.c
README           get_covered.c           maf_project.c         mz_preyama.h  speciesTree.h
README.md        get_standard_headers.c  maf_project_simple.c  mz_scores.c   tba.c
README2          lav2maf.c               maf_sort.c            mz_scores.h   tba.pdf
align_util.c     maf.c                   maf_sort.h            mz_yama.c     tba_howto.pdf
align_util.h     maf.h                   maf_sort_main.c       mz_yama.h     util.c
all_bz.c         maf2fasta.c             maftop2tb.c           nib.c         util.h
auto_mz.c        maf2lav.c               maftop2tb.h           nib.h
blastzWrapper.c  mafFind.c               multi_util.c          pair2tb.c
chain.h          maf_checkThread.c       multi_util.h          seq.c
charvec.c        maf_order.c             multic.c              seq.h

(base):~/multiz$ make
gcc -Wall -Wextra -O0 all_bz.c util.c -o all_bz
gcc -Wall -Wextra -O0 lav2maf.c mz_scores.c maf.c util.c seq.c nib.c charvec.c multi_util.c -o lav2maf
lav2maf.c: In function ‘main’:
lav2maf.c:170:35: warning: ‘%s’ directive writing up to 499 bytes into a region of size between 300 and 499 [-Wformat-overflow=]
  170 |                 sprintf(src1, "%s.%s", name1, chr1);
      |                                   ^~          ~~~~
lav2maf.c:170:17: note: ‘sprintf’ output between 2 and 700 bytes into a destination of size 500
  170 |                 sprintf(src1, "%s.%s", name1, chr1);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lav2maf.c:174:35: warning: ‘%s’ directive writing up to 499 bytes into a region of size between 300 and 499 [-Wformat-overflow=]
  174 |                 sprintf(src2, "%s.%s", name2, chr2);
      |                                   ^~          ~~~~
lav2maf.c:174:17: note: ‘sprintf’ output between 2 and 700 bytes into a destination of size 500
  174 |                 sprintf(src2, "%s.%s", name2, chr2);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/cciVjisz.o:(.bss+0x0): multiple definition of `ss'; /tmp/cc0rrcUJ.o:(.bss+0x0): first defined here
/usr/bin/ld: /tmp/cciVjisz.o:(.bss+0x8): multiple definition of `gop'; /tmp/cc0rrcUJ.o:(.bss+0x8): first defined here
/usr/bin/ld: /tmp/cciVjisz.o:(.bss+0x10): multiple definition of `gap_open'; /tmp/cc0rrcUJ.o:(.bss+0x10): first defined here
/usr/bin/ld: /tmp/cciVjisz.o:(.bss+0x14): multiple definition of `gap_extend'; /tmp/cc0rrcUJ.o:(.bss+0x14): first defined here
/usr/bin/ld: /tmp/cchH9zy4.o:(.bss+0x0): multiple definition of `ss'; /tmp/cc0rrcUJ.o:(.bss+0x0): first defined here
/usr/bin/ld: /tmp/cchH9zy4.o:(.bss+0x8): multiple definition of `gop'; /tmp/cc0rrcUJ.o:(.bss+0x8): first defined here
/usr/bin/ld: /tmp/cchH9zy4.o:(.bss+0x10): multiple definition of `gap_open'; /tmp/cc0rrcUJ.o:(.bss+0x10): first defined here
/usr/bin/ld: /tmp/cchH9zy4.o:(.bss+0x14): multiple definition of `gap_extend'; /tmp/cc0rrcUJ.o:(.bss+0x14): first defined here
/usr/bin/ld: /tmp/ccYPd5tm.o:(.bss+0x0): multiple definition of `ss'; /tmp/cc0rrcUJ.o:(.bss+0x0): first defined here
/usr/bin/ld: /tmp/ccYPd5tm.o:(.bss+0x8): multiple definition of `gop'; /tmp/cc0rrcUJ.o:(.bss+0x8): first defined here
/usr/bin/ld: /tmp/ccYPd5tm.o:(.bss+0x10): multiple definition of `gap_open'; /tmp/cc0rrcUJ.o:(.bss+0x10): first defined here
/usr/bin/ld: /tmp/ccYPd5tm.o:(.bss+0x14): multiple definition of `gap_extend'; /tmp/cc0rrcUJ.o:(.bss+0x14): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:23: lav2maf] Error 1
(base):~/multiz$

Answer 1

[Pierre Lindenbaum]

how about using bioconda to install this software ? https://bioconda.github.io/recipes/multiz/README.html

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

[Santex]

I could install multiz from it! Thank you very much. Please help me out with the problem below.

I run multiz like below.

(myenv) takao2002@USER-4ST1H56EM6:~/lastz-1.04.22/data/202409$ /home/takao2002/miniconda3/envs/myenv/bin/multiz homoTAD_mus.chain homoTAD_gallus.chain homoTAD_alligator.chain homoTAD_xenopus.chain homoTAD_lepisosteus.chain homoTAD_petromyzon.chain        mus_gallus.chain mus_alligator.chain mus_xenopus.chain mus_lepisosteus.chain mus_petromyzon.chain        gallus_alligator.chain gallus_xenopus.chain gallus_lepisosteus.chain gallus_petromyzon.chain        alligator_xenopus.chain alligator_lepisosteus.chain alligator_petromyzon.chain        xenopus_lepisosteus.chain xenopus_petromyzon.chain lepisosteus_petromyzon.chain > final_alignment1.maf

multiz.v11.2:  -- aligning two files of alignment blocks where top rows are always the reference, reference in both files cannot have duplicats
args: [R=?] [M=?] file1 file2 v? [out1 out2] [nohead] [all]
        R(30) radius in dynamic programming.
        M(1) minimum output width.
        out1 out2(null) null: stdout; out1 out2: file names for collecting unused input.
        nohead(null) null: output maf header; nohead: not to output maf header.
        all(null) null: not to output single-row blocks; all: output all blocks.

(myenv) takao2002@USER-4ST1H56EM6:~/lastz-1.04.22/data/202409$ ls 

After running multiz, the output maf file was 0kb. I checked the input files which is ".chain". All the input files were 1kb and the contents were same except for the last line. Is this normal? or should I start with chaining?

This is the contents of ".chain" file.

##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 ##gapPenalties=axtChain O=400 E=30

lastz.v1.04.22 --format=axt

hsp_threshold = 3000

gapped_threshold = 3000

x_drop = 910

y_drop = 9400

gap_open_penalty = 400

gap_extend_penalty = 30

A C G T

A 91 -114 -31 -123

C -114 100 -125 -31

G -31 -125 100 -114

T -123 -31 -114 91

chain 1073 Homo 16899100 + 436709 436731 Mus 34932950 - 1374067 1374089 1 22

[GenoMax]

Please do not ask questions unrelated to the original post in this thread. Post a new question.

[Santex]

I'm sorry. I post a new question.