error when run the duet demo data

[luckyvivi]

Hi Dr. Zhou,
Thanks for develop duet, I've successfully installed duet according to your instruction:

git clone https://github.com/yekaizhou/duet.git
cd duet && pip3 install .

But when I run on the demo data, it comes up with an error:

$duet duet_demo_data/HG00733_hg19_chr21.bam duet_demo_data/hg19_chr21.fa results
10:10:19 [INFO] ************************* DUET STARTED *************************
10:10:19 [INFO] ************************* SNP CALLING STARTED *************************
sh: line 1: run_clair3.sh: command not found
10:10:19 [INFO] ************************* SNP CALLING COMPLETED IN 0.007s *************************
10:10:19 [INFO] ************************* SV CALLING STARTED *************************
2022-12-09 10:10:19,723 [INFO] Running /usr/local/bin/cuteSV --genotype --report_readid duet_demo_data/HG00733_hg19_chr21.bam duet_demo_data/hg19_chr21.fa results/sv_calling/variants.vcf results/sv_calling/ -t 4 -s 2 -l 50
2022-12-09 10:10:19,724 [INFO] The total number of chromsomes: 86
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2022-12-09 10:10:19,798 [INFO] Skip 20:40000000-50000000.
2022-12-09 10:10:19,798 [INFO] Skip 20:50000000-60000000.
2022-12-09 10:10:19,799 [INFO] Skip 20:60000000-63025520.
2022-12-09 10:10:20,179 [INFO] Finished 21:0-10000000.
2022-12-09 10:10:24,869 [INFO] Finished 21:10000000-20000000.
2022-12-09 10:10:24,879 [INFO] Skip 22:0-10000000.
2022-12-09 10:10:24,880 [INFO] Skip 22:10000000-20000000.
2022-12-09 10:10:24,880 [INFO] Skip 22:20000000-30000000.
2022-12-09 10:10:24,881 [INFO] Skip 22:30000000-40000000.
2022-12-09 10:10:24,882 [INFO] Skip 22:40000000-50000000.
2022-12-09 10:10:24,882 [INFO] Skip 22:50000000-51304566.
2022-12-09 10:10:24,883 [INFO] Skip X:0-10000000.
2022-12-09 10:10:24,883 [INFO] Skip X:10000000-20000000.
2022-12-09 10:10:24,884 [INFO] Skip X:20000000-30000000.
2022-12-09 10:10:24,885 [INFO] Skip X:30000000-40000000.
2022-12-09 10:10:24,885 [INFO] Skip X:40000000-50000000.
2022-12-09 10:10:24,886 [INFO] Skip X:50000000-60000000.
2022-12-09 10:10:24,886 [INFO] Skip X:60000000-70000000.
2022-12-09 10:10:24,887 [INFO] Skip X:70000000-80000000.
2022-12-09 10:10:24,888 [INFO] Skip X:80000000-90000000.
2022-12-09 10:10:24,888 [INFO] Skip X:90000000-100000000.
2022-12-09 10:10:24,889 [INFO] Skip X:100000000-110000000.
2022-12-09 10:10:24,889 [INFO] Skip X:110000000-120000000.
2022-12-09 10:10:24,890 [INFO] Skip X:120000000-130000000.
2022-12-09 10:10:24,891 [INFO] Skip X:130000000-140000000.
2022-12-09 10:10:24,891 [INFO] Skip X:140000000-150000000.
2022-12-09 10:10:24,892 [INFO] Skip X:150000000-155270560.
2022-12-09 10:10:24,892 [INFO] Skip Y:0-10000000.
2022-12-09 10:10:24,893 [INFO] Skip Y:10000000-20000000.
2022-12-09 10:10:24,894 [INFO] Skip Y:20000000-30000000.
2022-12-09 10:10:24,894 [INFO] Skip Y:30000000-40000000.
2022-12-09 10:10:24,895 [INFO] Skip Y:40000000-50000000.
2022-12-09 10:10:24,896 [INFO] Skip Y:50000000-59373566.
2022-12-09 10:10:24,896 [INFO] Skip MT:0-16569.
2022-12-09 10:10:24,897 [INFO] Skip GL000207.1:0-4262.
2022-12-09 10:10:24,897 [INFO] Skip GL000226.1:0-15008.
2022-12-09 10:10:24,898 [INFO] Skip GL000229.1:0-19913.
2022-12-09 10:10:24,899 [INFO] Skip GL000231.1:0-27386.
2022-12-09 10:10:24,899 [INFO] Skip GL000210.1:0-27682.
2022-12-09 10:10:24,900 [INFO] Skip GL000239.1:0-33824.
2022-12-09 10:10:24,900 [INFO] Skip GL000235.1:0-34474.
2022-12-09 10:10:24,901 [INFO] Skip GL000201.1:0-36148.
2022-12-09 10:10:24,902 [INFO] Skip GL000247.1:0-36422.
2022-12-09 10:10:24,902 [INFO] Skip GL000245.1:0-36651.
2022-12-09 10:10:24,903 [INFO] Skip GL000197.1:0-37175.
2022-12-09 10:10:24,903 [INFO] Skip GL000203.1:0-37498.
2022-12-09 10:10:24,904 [INFO] Skip GL000246.1:0-38154.
2022-12-09 10:10:24,905 [INFO] Skip GL000249.1:0-38502.
2022-12-09 10:10:24,905 [INFO] Skip GL000196.1:0-38914.
2022-12-09 10:10:24,906 [INFO] Skip GL000248.1:0-39786.
2022-12-09 10:10:24,907 [INFO] Skip GL000244.1:0-39929.
2022-12-09 10:10:24,907 [INFO] Skip GL000238.1:0-39939.
2022-12-09 10:10:24,908 [INFO] Skip GL000202.1:0-40103.
2022-12-09 10:10:24,908 [INFO] Skip GL000234.1:0-40531.
2022-12-09 10:10:24,909 [INFO] Skip GL000232.1:0-40652.
2022-12-09 10:10:24,910 [INFO] Skip GL000206.1:0-41001.
2022-12-09 10:10:24,910 [INFO] Skip GL000240.1:0-41933.
2022-12-09 10:10:24,911 [INFO] Skip GL000236.1:0-41934.
2022-12-09 10:10:24,911 [INFO] Skip GL000241.1:0-42152.
2022-12-09 10:10:24,912 [INFO] Skip GL000243.1:0-43341.
2022-12-09 10:10:24,913 [INFO] Skip GL000242.1:0-43523.
2022-12-09 10:10:24,913 [INFO] Skip GL000230.1:0-43691.
2022-12-09 10:10:24,914 [INFO] Skip GL000237.1:0-45867.
2022-12-09 10:10:24,914 [INFO] Skip GL000233.1:0-45941.
2022-12-09 10:10:24,915 [INFO] Skip GL000204.1:0-81310.
2022-12-09 10:10:24,916 [INFO] Skip GL000198.1:0-90085.
2022-12-09 10:10:24,916 [INFO] Skip GL000208.1:0-92689.
2022-12-09 10:10:24,917 [INFO] Skip GL000191.1:0-106433.
2022-12-09 10:10:24,917 [INFO] Skip GL000227.1:0-128374.
2022-12-09 10:10:24,918 [INFO] Skip GL000228.1:0-129120.
2022-12-09 10:10:24,919 [INFO] Skip GL000214.1:0-137718.
2022-12-09 10:10:24,919 [INFO] Skip GL000221.1:0-155397.
2022-12-09 10:10:24,920 [INFO] Skip GL000209.1:0-159169.
2022-12-09 10:10:24,921 [INFO] Skip GL000218.1:0-161147.
2022-12-09 10:10:24,921 [INFO] Skip GL000220.1:0-161802.
2022-12-09 10:10:24,922 [INFO] Skip GL000213.1:0-164239.
2022-12-09 10:10:24,922 [INFO] Skip GL000211.1:0-166566.
2022-12-09 10:10:24,923 [INFO] Skip GL000199.1:0-169874.
2022-12-09 10:10:24,924 [INFO] Skip GL000217.1:0-172149.
2022-12-09 10:10:24,924 [INFO] Skip GL000216.1:0-172294.
2022-12-09 10:10:24,925 [INFO] Skip GL000215.1:0-172545.
2022-12-09 10:10:24,925 [INFO] Skip GL000205.1:0-174588.
2022-12-09 10:10:24,926 [INFO] Skip GL000219.1:0-179198.
2022-12-09 10:10:24,927 [INFO] Skip GL000224.1:0-179693.
2022-12-09 10:10:24,927 [INFO] Skip GL000223.1:0-180455.
2022-12-09 10:10:24,928 [INFO] Skip GL000195.1:0-182896.
2022-12-09 10:10:24,928 [INFO] Skip GL000212.1:0-186858.
2022-12-09 10:10:24,929 [INFO] Skip GL000222.1:0-186861.
2022-12-09 10:10:24,930 [INFO] Skip GL000200.1:0-187035.
2022-12-09 10:10:24,930 [INFO] Skip GL000193.1:0-189789.
2022-12-09 10:10:24,931 [INFO] Skip GL000194.1:0-191469.
2022-12-09 10:10:24,932 [INFO] Skip GL000225.1:0-211173.
2022-12-09 10:10:24,932 [INFO] Skip GL000192.1:0-547496.
2022-12-09 10:10:24,933 [INFO] Skip NC_007605:0-171823.
2022-12-09 10:10:24,933 [INFO] Skip hs37d5:0-10000000.
2022-12-09 10:10:24,934 [INFO] Skip hs37d5:10000000-20000000.
2022-12-09 10:10:24,935 [INFO] Skip hs37d5:20000000-30000000.
2022-12-09 10:10:24,935 [INFO] Skip hs37d5:30000000-35477943.
2022-12-09 10:10:25,647 [INFO] Finished 21:20000000-30000000.
2022-12-09 10:10:25,934 [INFO] Finished 21:40000000-48129895.
2022-12-09 10:10:26,028 [INFO] Finished 21:30000000-40000000.
2022-12-09 10:10:26,042 [INFO] Rebuilding signatures of structural variants.
2022-12-09 10:10:26,233 [INFO] Clustering structural variants.
2022-12-09 10:10:26,257 [INFO] Finished hs37d5:INV.
2022-12-09 10:10:26,342 [INFO] Finished 21:INV.
2022-12-09 10:10:26,351 [INFO] Finished X:DUP.
2022-12-09 10:10:26,359 [INFO] Finished hs37d5:DUP.
2022-12-09 10:10:26,360 [INFO] Finished 1-14:TRA/BND.
2022-12-09 10:10:26,360 [INFO] Finished 1-21:TRA/BND.
2022-12-09 10:10:26,361 [INFO] Finished 1-22:TRA/BND.
2022-12-09 10:10:26,361 [INFO] Finished 1-Y:TRA/BND.
2022-12-09 10:10:26,363 [INFO] Finished 1-hs37d5:TRA/BND.
2022-12-09 10:10:26,363 [INFO] Finished 10-21:TRA/BND.
2022-12-09 10:10:26,364 [INFO] Finished 10-8:TRA/BND.
2022-12-09 10:10:26,364 [INFO] Finished 10-Y:TRA/BND.
2022-12-09 10:10:26,365 [INFO] Finished 10-hs37d5:TRA/BND.
2022-12-09 10:10:26,369 [INFO] Finished 21:DUP.
2022-12-09 10:10:26,370 [INFO] Finished 12-2:TRA/BND.
2022-12-09 10:10:26,370 [INFO] Finished 12-20:TRA/BND.
2022-12-09 10:10:26,395 [INFO] Finished 11-21:TRA/BND.
2022-12-09 10:10:26,395 [INFO] Finished 12-4:TRA/BND.
2022-12-09 10:10:26,396 [INFO] Finished 12-6:TRA/BND.
2022-12-09 10:10:26,396 [INFO] Finished 12-7:TRA/BND.
2022-12-09 10:10:26,397 [INFO] Finished 12-hs37d5:TRA/BND.
2022-12-09 10:10:26,398 [INFO] Finished 13-21:TRA/BND.
2022-12-09 10:10:26,398 [INFO] Finished 13-6:TRA/BND.
2022-12-09 10:10:26,399 [INFO] Finished 13-hs37d5:TRA/BND.
2022-12-09 10:10:26,400 [INFO] Finished 14-15:TRA/BND.
2022-12-09 10:10:26,400 [INFO] Finished 14-21:TRA/BND.
2022-12-09 10:10:26,401 [INFO] Finished 15-20:TRA/BND.
2022-12-09 10:10:26,402 [INFO] Finished 12-21:TRA/BND.
2022-12-09 10:10:26,403 [INFO] Finished 15-22:TRA/BND.
2022-12-09 10:10:26,403 [INFO] Finished 15-3:TRA/BND.
2022-12-09 10:10:26,404 [INFO] Finished 16-21:TRA/BND.
2022-12-09 10:10:26,405 [INFO] Finished 17-21:TRA/BND.
2022-12-09 10:10:26,405 [INFO] Finished 17-3:TRA/BND.
2022-12-09 10:10:26,406 [INFO] Finished 17-hs37d5:TRA/BND.
2022-12-09 10:10:26,406 [INFO] Finished 15-21:TRA/BND.
2022-12-09 10:10:26,406 [INFO] Finished 18-21:TRA/BND.
2022-12-09 10:10:26,406 [INFO] Finished 19-21:TRA/BND.
2022-12-09 10:10:26,407 [INFO] Finished 2-9:TRA/BND.
2022-12-09 10:10:26,407 [INFO] Finished 2-GL000212.1:TRA/BND.
2022-12-09 10:10:26,408 [INFO] Finished 2-hs37d5:TRA/BND.
2022-12-09 10:10:26,409 [INFO] Finished 20-21:TRA/BND.
2022-12-09 10:10:26,409 [INFO] Finished 20-hs37d5:TRA/BND.
2022-12-09 10:10:26,442 [INFO] Finished 2-21:TRA/BND.
2022-12-09 10:10:26,443 [INFO] Finished 21-3:TRA/BND.
2022-12-09 10:10:26,443 [INFO] Finished 21-4:TRA/BND.
2022-12-09 10:10:26,444 [INFO] Finished 21-5:TRA/BND.
2022-12-09 10:10:26,444 [INFO] Finished 21-6:TRA/BND.
2022-12-09 10:10:26,528 [INFO] Finished 21-22:TRA/BND.
2022-12-09 10:10:26,528 [INFO] Finished 21-8:TRA/BND.
2022-12-09 10:10:26,558 [INFO] Finished 21-9:TRA/BND.
2022-12-09 10:10:26,558 [INFO] Finished 21-GL000199.1:TRA/BND.
2022-12-09 10:10:26,559 [INFO] Finished 21-GL000210.1:TRA/BND.
2022-12-09 10:10:26,588 [INFO] Finished 21-GL000212.1:TRA/BND.
2022-12-09 10:10:26,615 [INFO] Finished 21-7:TRA/BND.
2022-12-09 10:10:26,622 [INFO] Finished 21-GL000220.1:TRA/BND.
2022-12-09 10:10:26,622 [INFO] Finished 21-GL000226.1:TRA/BND.
2022-12-09 10:10:26,623 [INFO] Finished 21-GL000237.1:TRA/BND.
2022-12-09 10:10:26,623 [INFO] Finished 21-X:TRA/BND.
2022-12-09 10:10:26,636 [INFO] Finished 21-GL000216.1:TRA/BND.
2022-12-09 10:10:26,674 [INFO] Finished 21-Y:TRA/BND.
2022-12-09 10:10:26,675 [INFO] Finished 22-5:TRA/BND.
2022-12-09 10:10:26,676 [INFO] Finished 22-GL000210.1:TRA/BND.
2022-12-09 10:10:26,677 [INFO] Finished 22-hs37d5:TRA/BND.
2022-12-09 10:10:26,678 [INFO] Finished 3-6:TRA/BND.
2022-12-09 10:10:26,678 [INFO] Finished 3-X:TRA/BND.
2022-12-09 10:10:26,679 [INFO] Finished 4-7:TRA/BND.
2022-12-09 10:10:26,679 [INFO] Finished 4-X:TRA/BND.
2022-12-09 10:10:26,680 [INFO] Finished 5-GL000210.1:TRA/BND.
2022-12-09 10:10:26,680 [INFO] Finished 6-hs37d5:TRA/BND.
2022-12-09 10:10:26,681 [INFO] Finished 7-GL000237.1:TRA/BND.
2022-12-09 10:10:26,681 [INFO] Finished 8-hs37d5:TRA/BND.
2022-12-09 10:10:26,682 [INFO] Finished GL000212.1-hs37d5:TRA/BND.
2022-12-09 10:10:26,683 [INFO] Finished GL000220.1-GL000243.1:TRA/BND.
2022-12-09 10:10:26,683 [INFO] Finished GL000220.1-hs37d5:TRA/BND.
2022-12-09 10:10:26,683 [INFO] Finished GL000237.1-hs37d5:TRA/BND.
2022-12-09 10:10:26,684 [INFO] Finished GL000243.1-hs37d5:TRA/BND.
2022-12-09 10:10:26,684 [INFO] Finished X-hs37d5:TRA/BND.
2022-12-09 10:10:26,685 [INFO] Finished Y-hs37d5:TRA/BND.
2022-12-09 10:10:26,751 [INFO] Finished 21:INS.
2022-12-09 10:10:26,894 [INFO] Finished 21:DEL.
2022-12-09 10:10:27,315 [INFO] Finished 21-hs37d5:TRA/BND.
2022-12-09 10:10:27,322 [INFO] Writing to your output file.
2022-12-09 10:10:27,326 [INFO] Loading reference genome...
Traceback (most recent call last):
  File "/usr/local/bin/cuteSV", line 4, in <module>
    __import__('pkg_resources').run_script('cuteSV==2.0.2', 'cuteSV')
  File "/usr/local/lib/python3.10/dist-packages/pkg_resources/__init__.py", line 651, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python3.10/dist-packages/pkg_resources/__init__.py", line 1448, in run_script
    exec(code, namespace, namespace)
  File "/usr/local/lib/python3.10/dist-packages/cuteSV-2.0.2-py3.10.egg/EGG-INFO/scripts/cuteSV", line 888, in <module>
    run(sys.argv[1:])
  File "/usr/local/lib/python3.10/dist-packages/cuteSV-2.0.2-py3.10.egg/EGG-INFO/scripts/cuteSV", line 884, in run
    main_ctrl(args, argv)
  File "/usr/local/lib/python3.10/dist-packages/cuteSV-2.0.2-py3.10.egg/EGG-INFO/scripts/cuteSV", line 862, in main_ctrl
    generate_output(args, semi_result, contigINFO, argv, ref_g)
  File "/usr/local/lib/python3.10/dist-packages/cuteSV-2.0.2-py3.10.egg/cuteSV/cuteSV_genotype.py", line 287, in generate_output
    REF = str(ref_g[i[0]].seq[int(i[2])]),
KeyError: 'hs37d5'
10:10:27 [INFO] ************************* SV CALLING COMPLETED IN 8.516s *************************
10:10:27 [INFO] ************************* SNP PHASING STARTED *************************
[E::idx_find_and_load] Could not retrieve index file for 'results/snp_calling/pileup.vcf.gz'
Could not load .tbi index of results/snp_calling/pileup.vcf.gz: No such file or directory
Traceback (most recent call last):
  File "/home/disk2/vivi/.local/bin/duet", line 31, in <module>
    main(sys.argv[1:])
  File "/home/disk2/vivi/.local/bin/duet", line 25, in main
    snp_phasing(args.OUTPUT, args.REFERENCE, args.BAM, args.thread)
  File "/home/disk2/vivi/.local/lib/python3.10/site-packages/duet/snp_phasing.py", line 17, in snp_phasing
    ctgs = subprocess.check_output(shlex.split('tabix --list-chroms ' + pileup_vcf_path)).decode('ascii').split('\n')[:-1]
  File "/usr/lib/python3.10/subprocess.py", line 420, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/usr/lib/python3.10/subprocess.py", line 524, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['tabix', '--list-chroms', 'results/snp_calling/pileup.vcf.gz']' returned non-zero exit status 1.

[yekaizhou]

Hi @luckyvivi,

It looks to me that some of the dependencies have not been installed properly.
Have you run conda install -c bioconda clair3=0.1.12 sniffles=2.0.7 cutesv=2.0.2 svim=1.4.2 bcftools=1.8 -y before cloning and installing duet?

Yekai

[luckyvivi]

Hi @luckyvivi,

It looks to me that some of the dependencies have not been installed properly. Have you run conda install -c bioconda clair3=0.1.12 sniffles=2.0.7 cutesv=2.0.2 svim=1.4.2 bcftools=1.8 -y before cloning and installing duet?

Yekai

Hi Dr. Zhou,

When I run conda install -c bioconda clair3=0.1.12 sniffles=2.0.7 cutesv=2.0.2 svim=1.4.2 bcftools=1.8 -y, it seems to have some error. Could you please help me install duet properlly.

$conda create -n duet -c bioconda clair3=0.1.12 sniffles=2.0.7 cutesv=2.0.2 svim=1.4.2 bcftools=1.8 -y && conda activate duet
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
Building graph of deps:   0%|                                                                                                            | 0/9 [00:Examining cutesv=2.0.2:   0%|                                                                                                            | 0/9 [00:Examining bcftools=1.8:  11%|███████████                                                                                         | 1/9 [00:00<00:00Examining @/linux-64::__glibc==2.35=0:  22%|██████████████████▉                                                                  | 2/9 [00:00<00:00Examining @/linux-64::__glibc==2.35=0:  33%|████████████████████████████▎                                                        | 3/9 [00:00<00:00Examining @/linux-64::__unix==0=0:  33%|█████████████████████████████▋                                                           | 3/9 [00:00<00:00Examining @/linux-64::__archspec==1=x86_64:  44%|███████████████████████████████████▌                                            | 4/9 [00:00<00:00Examining sniffles=2.0.7:  56%|██████████████████████████████████████████████████████▍                                           | 5/9 [00:00<00:00Examining @/linux-64::__linux==5.15.0=0:  67%|███████████████████████████████████████████████████████▎                           | 6/9 [00:00<00:00Examining clair3=0.1.12:  78%|█████████████████████████████████████████████████████████████████████████████                      | 7/9 [00:00<00:00Examining svim=1.4.2:  89%|██████████████████████████████████████████████████████████████████████████████████████████▋           | 8/9 [00:00<00:00Examining svim=1.4.2: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:00<00:00                                                                                                                                                   Determining conflicts:   0%|                                                                                                             | 0/9 [00:Examining conflict for cutesv clair3:   0%|                                                                                              | 0/9 [00:Examining conflict for cutesv clair3 svim:  11%|█████████                                                                        | 1/9 [00:00<00:03Examining conflict for cutesv clair3 svim:  22%|██████████████████                                                               | 2/9 [00:00<00:01Examining conflict for cutesv bcftools sniffles svim:  22%|███████████████▌                                                      | 2/9 [00:06<00:01Examining conflict for cutesv bcftools sniffles svim:  33%|███████████████████████▎                                              | 3/9 [00:06<00:16Examining conflict for cutesv clair3 sniffles svim:  33%|████████████████████████                                                | 3/9 [00:07<00:16Examining conflict for cutesv clair3 sniffles svim:  44%|████████████████████████████████                                        | 4/9 [00:07<00:09Examining conflict for cutesv bcftools sniffles clair3 svim:  44%|████████████████████████████                                   | 4/9 [00:14<00:09Examining conflict for cutesv bcftools sniffles clair3 svim:  56%|███████████████████████████████████                            | 5/9 [00:14<00:15Examining conflict for cutesv sniffles svim:  56%|███████████████████████████████████████████▉                                   | 5/9 [00:18<00:15Examining conflict for cutesv sniffles svim:  67%|████████████████████████████████████████████████████▋                          | 6/9 [00:18<00:11Examining conflict for bcftools sniffles svim:  67%|███████████████████████████████████████████████████▎                         | 6/9 [00:19<00:11Examining conflict for bcftools sniffles svim:  78%|███████████████████████████████████████████████████████████▉                 | 7/9 [00:19<00:06Examining conflict for bcftools __glibc:  78%|████████████████████████████████████████████████████████████████▌                  | 7/9 [00:20<00:06Examining conflict for bcftools __glibc:  89%|█████████████████████████████████████████████████████████████████████████▊         | 8/9 [00:20<00:02Examining conflict for clair3 svim:  89%|██████████████████████████████████████████████████████████████████████████████▏         | 8/9 [00:20<00:02                                                                                                                                                 failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package tk conflicts for:
clair3=0.1.12 -> python=3.9.0 -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.11,<8.7.0a0']
sniffles=2.0.7 -> python[version='>=3.7'] -> tk[version='>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']
svim=1.4.2 -> matplotlib-base -> tk[version='8.6.*|>=8.6.10,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.7,<8.7.0a0']
cutesv=2.0.2 -> python[version='>=3'] -> tk[version='8.6.*|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']

Package libgcc-ng conflicts for:
bcftools=1.8 -> libgcc-ng[version='>=4.9']
svim=1.4.2 -> matplotlib-base -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.5.0|>=9.3.0|>=7.3.0|>=9.4.0|>=4.9|>=7.2.0|>=12']
bcftools=1.8 -> bzip2[version='>=1.0.6,<2.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.2.0|>=7.3.0|>=7.5.0']
cutesv=2.0.2 -> biopython -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.2.0|>=7.3.0|>=7.5.0|>=12|>=9.4.0|>=9.3.0|>=4.9']
sniffles=2.0.7 -> pysam -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
clair3=0.1.12 -> bzip2[version='>=1.0.8,<2.0a0'] -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=7.3.0|>=7.5.0|>=7.2.0']
clair3=0.1.12 -> libgcc-ng[version='>=12']

Package libgcc conflicts for:
sniffles=2.0.7 -> pysam -> libgcc
bcftools=1.8 -> libgcc
svim=1.4.2 -> minimap2 -> libgcc

Package numpy-base conflicts for:
clair3=0.1.12 -> numpy -> 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svim=1.4.2 -> numpy -> numpy-base[version='1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.17.2.*|1.17.3.*|1.17.4.*|1.18.1.*|1.18.5.*|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.23.1|1.23.1|1.23.1|1.23.1|1.23.1|1.23.1|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.4|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|>=1.9.3,<2.0a0|1.17.0|1.17.0|1.17.0|1.17.0',build='py36h2f8d375_0|py37h2f8d375_0|py37hde5b4d6_0|py27h2b20989_6|py36h2b20989_6|py37h2b20989_6|py37hdbf6ddf_6|py27hdbf6ddf_6|py27hdbf6ddf_7|py36hdbf6ddf_7|py36h2b20989_7|py35hdbf6ddf_7|py37h2b20989_7|py37h2b20989_7|py36h2b20989_7|py27hdbf6ddf_7|py36hdbf6ddf_7|py37hdbf6ddf_7|py27h2b20989_8|py27hdbf6ddf_8|py35hdbf6ddf_8|py36h7cdd4dd_9|py27h7cdd4dd_9|py36h81de0dd_9|py27h74e8950_9|py27h81de0dd_9|py35h81de0dd_9|py37h74e8950_10|py35h74e8950_10|py27h74e8950_10|py36h74e8950_10|py37h81de0dd_10|py36h81de0dd_10|py35h81de0dd_10|py37h2f8d375_10|py36h2f8d375_10|py27h2f8d375_10|py37h2f8d375_11|py27h2f8d375_11|py36h2f8d375_11|py36hde5b4d6_11|py37h2f8d375_12|py37hde5b4d6_12|py36hde5b4d6_12|py36h0ea5e3f_1|py35h0ea5e3f_1|py27h9be14a7_1|py35h9be14a7_1|py27h2b20989_0|py27hdbf6ddf_0|py36hdbf6ddf_0|py35hdbf6ddf_0|py27h2b20989_0|py36hdbf6ddf_0|py35hdbf6ddf_0|py36h2b20989_1|py36hdbf6ddf_1|py27h2b20989_2|py36h2b20989_2|py37h2b20989_2|py37hdbf6ddf_2|py37h2b20989_3|py37hdbf6ddf_3|py36hdbf6ddf_3|py27h2b20989_3|py27hdbf6ddf_3|py27h2b20989_4|py27hdbf6ddf_4|py37hdbf6ddf_4|py35h2b20989_4|py35h2f8d375_4|py36h2f8d375_4|py35h81de0dd_4|py38h2f8d375_4|py38hde5b4d6_4|py27hde5b4d6_5|py37hde5b4d6_5|py36hde5b4d6_5|py37h7cdd4dd_0|py35h7cdd4dd_0|py27h3dfced4_0|py36h3dfced4_0|py37h3dfced4_0|py35h74e8950_0|py27h74e8950_0|py36h74e8950_0|py36h81de0dd_0|py27h81de0dd_0|py35h81de0dd_0|py35h2f8d375_0|py37h2f8d375_0|py27h2f8d375_0|py35h81de0dd_0|py36h2f8d375_0|py36h81de0dd_0|py27h2f8d375_1|py27h81de0dd_1|py37h81de0dd_1|py36h2f8d375_0|py37h2f8d375_0|py36h2f8d375_0|py36h81de0dd_0|py27hde5b4d6_0|py37hde5b4d6_0|py37hde5b4d6_0|py27hde5b4d6_0|py37h2f8d375_1|py27h2f8d375_1|py37hde5b4d6_1|py37h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py27h2f8d375_1|py36h2f8d375_1|py36h2f8d375_0|py27h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py27h2f8d375_0|py36h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py36h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py27h2f8d375_0|py27hde5b4d6_0|py37hde5b4d6_0|py36h2f8d375_0|py37hde5b4d6_0|py38hde5b4d6_0|py27h2f8d375_0|py27hde5b4d6_0|py39hfb011de_1|py39h41b4c56_3|py38h41b4c56_3|py37h41b4c56_3|py36h41b4c56_3|py38hdc34a94_3|py39hdc34a94_3|py38h75fe3a5_0|py38hfa32c7d_0|py37h75fe3a5_0|py37h75fe3a5_0|py38hfa32c7d_0|py37h4c65ebe_1|py39h21a3de8_1|py38h21a3de8_1|py37h34387ca_0|py38h34387ca_0|py38h7d8b39e_0|py39h7d8b39e_0|py38hfae3a4d_0|py39he2ba247_0|py37he2ba247_0|py38h39b7dee_0|py38h79a1101_0|py37h2b8c604_0|py39h2b8c604_0|py310h2b8c604_0|py38hb8be1f0_1|py37hb8be1f0_1|py37hf524024_1|py310hf2716ce_1|py31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cutesv=2.0.2 -> numpy -> numpy-base[version='1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.11.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.3|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.4|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.5|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.14.6|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.0|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.1|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.2|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.3|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.15.4|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.0|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.1|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.2|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.3|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.4|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.5|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.16.6|1.17.2.*|1.17.3.*|1.17.4.*|1.18.1.*|1.18.5.*|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.1|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.19.2|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.2|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.20.3|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.2|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.21.5|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.22.3|1.23.1|1.23.1|1.23.1|1.23.1|1.23.1|1.23.1|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.3|1.23.4|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|1.9.3|>=1.9.3,<2.0a0|1.17.0|1.17.0|1.17.0|1.17.0',build='py36h2f8d375_0|py37h2f8d375_0|py37hde5b4d6_0|py27h2b20989_6|py36h2b20989_6|py37h2b20989_6|py37hdbf6ddf_6|py27hdbf6ddf_6|py27hdbf6ddf_7|py36hdbf6ddf_7|py36h2b20989_7|py35hdbf6ddf_7|py37h2b20989_7|py37h2b20989_7|py36h2b20989_7|py27hdbf6ddf_7|py36hdbf6ddf_7|py37hdbf6ddf_7|py27h2b20989_8|py27hdbf6ddf_8|py35hdbf6ddf_8|py36h7cdd4dd_9|py27h7cdd4dd_9|py36h81de0dd_9|py27h74e8950_9|py27h81de0dd_9|py35h81de0dd_9|py37h74e8950_10|py35h74e8950_10|py27h74e8950_10|py36h74e8950_10|py37h81de0dd_10|py36h81de0dd_10|py35h81de0dd_10|py37h2f8d375_10|py36h2f8d375_10|py27h2f8d375_10|py37h2f8d375_11|py27h2f8d375_11|py36h2f8d375_11|py36hde5b4d6_11|py37h2f8d375_12|py37hde5b4d6_12|py36hde5b4d6_12|py36h0ea5e3f_1|py35h0ea5e3f_1|py27h9be14a7_1|py35h9be14a7_1|py27h2b20989_0|py27hdbf6ddf_0|py36hdbf6ddf_0|py35hdbf6ddf_0|py27h2b20989_0|py36hdbf6ddf_0|py35hdbf6ddf_0|py36h2b20989_1|py36hdbf6ddf_1|py27h2b20989_2|py36h2b20989_2|py37h2b20989_2|py37hdbf6ddf_2|py37h2b20989_3|py37hdbf6ddf_3|py36hdbf6ddf_3|py27h2b20989_3|py27hdbf6ddf_3|py27h2b20989_4|py27hdbf6ddf_4|py37hdbf6ddf_4|py35h2b20989_4|py35h2f8d375_4|py36h2f8d375_4|py35h81de0dd_4|py38h2f8d375_4|py38hde5b4d6_4|py27hde5b4d6_5|py37hde5b4d6_5|py36hde5b4d6_5|py37h7cdd4dd_0|py35h7cdd4dd_0|py27h3dfced4_0|py36h3dfced4_0|py37h3dfced4_0|py35h74e8950_0|py27h74e8950_0|py36h74e8950_0|py36h81de0dd_0|py27h81de0dd_0|py35h81de0dd_0|py35h2f8d375_0|py37h2f8d375_0|py27h2f8d375_0|py35h81de0dd_0|py36h2f8d375_0|py36h81de0dd_0|py27h2f8d375_1|py27h81de0dd_1|py37h81de0dd_1|py36h2f8d375_0|py37h2f8d375_0|py36h2f8d375_0|py36h81de0dd_0|py27hde5b4d6_0|py37hde5b4d6_0|py37hde5b4d6_0|py27hde5b4d6_0|py37h2f8d375_1|py27h2f8d375_1|py37hde5b4d6_1|py37h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py27h2f8d375_1|py36h2f8d375_1|py36h2f8d375_0|py27h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py27h2f8d375_0|py36h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py36h2f8d375_0|py37hde5b4d6_0|py27hde5b4d6_0|py27h2f8d375_0|py27hde5b4d6_0|py37hde5b4d6_0|py36h2f8d375_0|py37hde5b4d6_0|py38hde5b4d6_0|py27h2f8d375_0|py27hde5b4d6_0|py39hfb011de_1|py39h41b4c56_3|py38h41b4c56_3|py37h41b4c56_3|py36h41b4c56_3|py38hdc34a94_3|py39hdc34a94_3|py38h75fe3a5_0|py38hfa32c7d_0|py37h75fe3a5_0|py37h75fe3a5_0|py38hfa32c7d_0|py37h4c65ebe_1|py39h21a3de8_1|py38h21a3de8_1|py37h34387ca_0|py38h34387ca_0|py38h7d8b39e_0|py39h7d8b39e_0|py38hfae3a4d_0|py39he2ba247_0|py37he2ba247_0|py38h39b7dee_0|py38h79a1101_0|py37h2b8c604_0|py39h2b8c604_0|py310h2b8c604_0|py38hb8be1f0_1|py37hb8be1f0_1|py37hf524024_1|py310hf2716ce_1|py31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Package scipy conflicts for:
svim=1.4.2 -> networkx -> scipy[version='>=1.5,!=1.6.1']
svim=1.4.2 -> scipy
clair3=0.1.12 -> whatshap=1.4 -> scipy

Package python conflicts for:
cutesv=2.0.2 -> python[version='>=3']
cutesv=2.0.2 -> biopython -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.10,<3.11.0a0|>=3.6,<3.7.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']

Package libuuid conflicts for:
sniffles=2.0.7 -> python[version='>=3.7'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']
svim=1.4.2 -> python[version='>=3.6'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']
cutesv=2.0.2 -> python[version='>=3'] -> libuuid[version='>=1.0.3,<2.0a0|>=1.41.5,<2.0a0']

Package numpy conflicts for:
cutesv=2.0.2 -> biopython -> numpy[version='1.10.*|1.12.*|>=1.11.3,<2.0a0|>=1.9.3,<2.0a0|>=1.14.1,<2.0a0']
cutesv=2.0.2 -> numpy

Package bcftools conflicts for:
svim=1.4.2 -> pysam[version='>=0.15'] -> bcftools=1.9
bcftools=1.8
sniffles=2.0.7 -> pysam -> bcftools[version='1.3|1.3.1.*|1.3.1|1.5.*|1.6.*|1.6|1.7.*|1.9.*|>=1.4.1|>=1.4.1,<1.5|>=1.4,<1.5|>=1.3,<1.4|>=1.3']

Package biopython conflicts for:
cutesv=2.0.2 -> biopython
clair3=0.1.12 -> whatshap=1.4 -> biopython[version='>=1.73']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.35=0
  - feature:|@/linux-64::__glibc==2.35=0
  - bcftools=1.8 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']

Your installed version is: 2.35

[yekaizhou]

You should create another conda environment for processing with duet and its dependenciea.

Please remove the installed duet from your current path first:
pip3 uninstall duet

Then, please run the following commands one by one:

conda config --add channels bioconda && conda config --add channels conda-forge
conda create -n duet -c bioconda clair3=0.1.12 sniffles=2.0.7 cutesv=2.0.2 svim=1.4.2 bcftools=1.8 -y && conda activate duet
git clone https://github.com/yekaizhou/duet.git
cd duet && pip3 install .

Or you can choose to install duet from conda:

conda config --add channels bioconda && conda config --add channels conda-forge
conda create -n duet -c bioconda duet -y && conda activate duet

Please remember to run "conda activate duet" when you need to use duet next time.

Yekai

[luckyvivi]

You should create another conda environment for processing with duet and its dependenciea.

Please remove the installed duet from your current path first: pip3 uninstall duet

Then, please run the following commands one by one:

conda config --add channels bioconda && conda config --add channels conda-forge
conda create -n duet -c bioconda clair3=0.1.12 sniffles=2.0.7 cutesv=2.0.2 svim=1.4.2 bcftools=1.8 -y && conda activate duet
git clone https://github.com/yekaizhou/duet.git
cd duet && pip3 install .

Or you can choose to install duet from conda:

conda config --add channels bioconda && conda config --add channels conda-forge
conda create -n duet -c bioconda duet -y && conda activate duet

Please remember to run "conda activate duet" when you need to use duet next time.

Yekai

Thanks Yekai,

Thanks for your help solving this problem, duet runs smoothly on demo data and produce phased_sv.vcf. But on my own data, it stopped and show WARNING message

[WARNING] No contig intersection found, output header only in /home/disk2/vivi/workspace/20221208_Nanopore/01.ONT_minimap/MU4_q_Hap2.results/snp_calling/merge_output.vcf.gz

[yekaizhou]

Hi Xiaowen,

Could you tell me what kind of organism that you are sequencing of? Is it kind of fungi or something? Could you please tell me a bit more about your own data?

Yekai

[starsyi]

I also encountered the same problem and followed the instructions above to reinstall multiple times in a new environment. However, I still encountered an error when running the demo data, and it was the same error.

2023-08-29 11:12:33,727 [INFO] Loading reference genome...
Traceback (most recent call last):
  File "/home/wzm/soft/miniconda3/envs/duet/bin/cuteSV", line 877, in <module>
    run(sys.argv[1:])
  File "/home/wzm/soft/miniconda3/envs/duet/bin/cuteSV", line 873, in run
    main_ctrl(args, argv)
  File "/home/wzm/soft/miniconda3/envs/duet/bin/cuteSV", line 851, in main_ctrl
    generate_output(args, semi_result, contigINFO, argv, ref_g)
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/cuteSV/cuteSV_genotype.py", line 285, in generate_output
    REF = str(ref_g[i[0]].seq[int(i[2])]),
KeyError: 'hs37d5'
11:12:34 [INFO] ************************* SV CALLING COMPLETED IN 7.253s *************************
11:12:34 [INFO] ************************* SNP PHASING STARTED *************************
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:

  O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
  DOI https://doi.org/10.5281/zenodo.1146014

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice

To silence this citation notice: run 'parallel --citation' once.

Come on: You have run parallel 13 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?

This is WhatsHap 1.7 running under Python 3.9.0
Traceback (most recent call last):
  File "/home/wzm/soft/miniconda3/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1169, in main
    run_whatshap(**vars(args))
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 391, in run_whatshap
    PhasedVcfWriter(
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 1069, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 973, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/home/wzm/soft/miniconda3/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 873, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'results_3/snp_phasing/21.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:

  O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
  DOI https://doi.org/10.5281/zenodo.1146014

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice

To silence this citation notice: run 'parallel --citation' once.

Come on: You have run parallel 14 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?

tbx_index_build failed: results_3/snp_phasing/phased_21.vcf.gz
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:

  O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,
  DOI https://doi.org/10.5281/zenodo.1146014

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice

To silence this citation notice: run 'parallel --citation' once.

Come on: You have run parallel 15 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?

[E::hts_open_format] Failed to open file "results_3/snp_phasing/phased_21.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file results_3/snp_phasing/phased_21.vcf.gz: [Errno 2] could not open variant file `b'results_3/snp_phasing/phased_21.vcf.gz'`: No such file or directory
11:12:35 [INFO] ************************* SNP PHASING COMPLETED IN 1.025s *************************
11:12:35 [INFO] ************************* SV PHASING STARTED *************************
11:12:35 [INFO] create output .vcf file
11:12:35 [INFO] extract SNP signatures
11:12:35 [INFO] extract SV signatures
11:12:35 [INFO]   signatures extracted from 1
11:12:35 [INFO]   signatures extracted from 2
11:12:35 [INFO]   no signature from 3
11:12:35 [INFO]   no signature from 4
11:12:35 [INFO]   no signature from 5
11:12:35 [INFO]   no signature from 6
11:12:35 [INFO]   no signature from 7
11:12:35 [INFO]   no signature from 8
11:12:35 [INFO]   no signature from 9
11:12:35 [INFO]   no signature from 10
11:12:35 [INFO]   signatures extracted from 11
11:12:35 [INFO]   signatures extracted from 12
11:12:35 [INFO]   signatures extracted from 13
11:12:35 [INFO]   no signature from 14
11:12:35 [INFO]   signatures extracted from 15
11:12:35 [INFO]   no signature from 16
11:12:35 [INFO]   no signature from 17
11:12:35 [INFO]   no signature from 18
11:12:35 [INFO]   no signature from 19
11:12:35 [INFO]   no signature from 20
11:12:35 [INFO]   signatures extracted from 21
11:12:35 [INFO]   signatures extracted from 22
11:12:35 [INFO]   no signature from X
11:12:35 [INFO]   no signature from Y
11:12:35 [INFO] integrate read weight information
11:12:35 [INFO] calculate read weight statistics
11:12:35 [INFO] predict SV haplotypes in the callset
11:12:35 [INFO] write phased callset into .vcf file
11:12:35 [INFO] ************************* SV PHASING COMPLETED IN 0.205s *************************
11:12:35 [INFO] ************************* DUET FINISHED IN 383.609s *************************
11:12:35 [INFO] OUTPUT .VCF FILE AT results_3/phased_sv.vcf