How to compile Multiz
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Entering edit mode
16 days ago
Santex • 0

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$
LastZ Github Multiz • 416 views
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16 days ago

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

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

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I'm sorry. I post a new question.

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