Open hanyoupan opened 2 weeks ago
I'm trying to run parallel_singer on my data. Below is the error message I received. Would you please take a look? Thanks a lot.
in_vcf_path="../vcf/33_rats/06_s300/33_rats_mRatBN7.2_chr19_qual30_bsnp_rmm_rmh_mafgl0_s300" out_vcf_path="./chr19_s300/chr19_s300" ./singer-0.1.8-beta-linux-x86_64/parallel_singer -Ne 1e4 -m 1.2e-8 -vcf $in_vcf_path -output $out_vcf_path -n 33 -thin 300
Processing segment 0 Processing segment 1 Traceback (most recent call last): File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 118, in main() File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 114, in main ts = read_long_ARG(node_files, branch_files, mutation_files, block_coordinates) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 33, in read_long_ARG assert t >= min_time ^^^^^^^^^^^^^^^^^^^^ AssertionError Processing segment 0 Processing segment 1 Traceback (most recent call last): File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 118, in main() File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 114, in main ts = read_long_ARG(node_files, branch_files, mutation_files, block_coordinates) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 33, in read_long_ARG assert t >= min_time ^^^^^^^^^^^^^^^^^^^^ AssertionError
Here is my input file.
33_rats_mRatBN7.2_chr19_qual30_bsnp_rmm_rmh_mafgl0_s300.txt
hanyoupan
commented
2 weeks ago hanyoupan
commented
2 weeks ago
I'm trying to run parallel_singer on my data. Below is the error message I received. Would you please take a look? Thanks a lot.
My commands
in_vcf_path="../vcf/33_rats/06_s300/33_rats_mRatBN7.2_chr19_qual30_bsnp_rmm_rmh_mafgl0_s300" out_vcf_path="./chr19_s300/chr19_s300" ./singer-0.1.8-beta-linux-x86_64/parallel_singer -Ne 1e4 -m 1.2e-8 -vcf $in_vcf_path -output $out_vcf_path -n 33 -thin 300
Error message
Processing segment 0 Processing segment 1 Traceback (most recent call last): File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 118, in
main()
File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 114, in main
ts = read_long_ARG(node_files, branch_files, mutation_files, block_coordinates)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 33, in read_long_ARG
assert t >= min_time
^^^^^^^^^^^^^^^^^^^^
AssertionError
Processing segment 0
Processing segment 1
Traceback (most recent call last):
File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 118, in
main()
File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 114, in main
ts = read_long_ARG(node_files, branch_files, mutation_files, block_coordinates)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/c/hanyou_c/projects/2024-02-21_ancestral_haplotypes_3/singer/singer-0.1.8-beta-linux-x86_64/convert_long_ARG.py", line 33, in read_long_ARG
assert t >= min_time
^^^^^^^^^^^^^^^^^^^^
AssertionError