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
