No module found error

[Michaelijesse]

Traceback (most recent call last): File "/home/centos/miniconda3/envs/tb-profiler/bin/tb-profiler", line 562, in args.func(args) File "/home/centos/miniconda3/envs/tb-profiler/bin/tb-profiler", line 110, in main_profile results.update(pp.run_profiler(args)) File "/home/centos/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/cli.py", line 58, in run_profiler results = bam_profiler( File "/home/centos/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/profiler.py", line 35, in bam_profiler ann_vcf_obj = vcf_obj.run_snpeff(conf["snpEff_db"],conf["ref"],conf["gff"],rename_chroms= conf.get("chromosome_conversion",None)) File "/home/centos/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/vcf.py", line 134, in run_snpeff run_cmd("bcftools view -c 1 -a %(filename)s | bcftools view -v snps | combine_vcf_variants.py --ref %(ref_file)s --gff %(gff_file)s | %(rename_cmd)s snpEff ann %(snpeff_data_dir_opt)s -noLog -noStats %(db)s - %(re_rename_cmd)s | bcftools sort -Oz -o %(tmp_file1)s && bcftools index %(tmp_file1)s" % vars(self)) File "/home/centos/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/utils.py", line 392, in run_cmd raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode())) ValueError: Command Failed: /bin/bash -c set -o pipefail; bcftools view -c 1 -a /home/centos/Michael/MTB_Manu/reads/40reads/621cb0a0-1841-43a3-b286-2edaa1b2ed4b.targets.vcf.gz | bcftools view -v snps | combine_vcf_variants.py --ref /home/centos/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.fasta --gff /home/centos/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.gff | snpEff ann -dataDir /home/centos/miniconda3/envs/tb-profiler/share/snpeff-5.2-0/data -noLog -noStats Mycobacterium_tuberculosis_h37rv - | bcftools sort -Oz -o /home/centos/Michael/MTB_Manu/reads/40reads/ad682830-2309-43d8-ab98-01e9a810d4e7.vcf.gz && bcftools index /home/centos/Michael/MTB_Manu/reads/40reads/ad682830-2309-43d8-ab98-01e9a810d4e7.vcf.gz stderr: Writing to /tmp/bcftools.HjRWaL Traceback (most recent call last): File "/usr/local/bin/combine_vcf_variants.py", line 6, in import pathogenprofiler as pp ModuleNotFoundError: No module named 'pathogenprofiler' [E::bcf_hdr_read] Input is not detected as bcf or vcf format Could not read VCF/BCF headers from - Cleaning