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16 hours 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$
I could install multiz from it! Thank you very much. Please help me out with the problem below.
I run multiz like below.
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.
Please do not ask questions unrelated to the original post in this thread. Post a new question.
I'm sorry. I post a new question.