Mamba build of tb-profiler failing

[noahaus]

Hello Jody, I'm throwing my hands in the air and looking for some assistance as to why I'm getting strange behavior from tb-profiler. I have created a conda environment (tb-profiler) which uses mamba to download tb-profiler and any of its dependencies. Everything downloaded and looks standard. However, the wacky stuff happens when I try and do a simple 'profile'.

Below I included the error logs, and also some speculations as to what I find odd. Hopefully this can be helpful in figuring out what is going on?

• python is reverted to 3.9 version
• tested both tb-profiler versions 4.4.0 and 5.0.0, problem persists
• This is pretty odd to me, some of the paths to reference files have a double '//' which I am suspicious about? i.e.

  ref': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta', 'gff': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.gff', 'bed': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.bed'

  I'm worried that this affects the reading of the files. It gets to the 'samclip' step, and maybe this is where the issue is, but wanted to give you an idea.

• it gets to the sam-clip step and then fails, as seen in the error logs.

[noahaus]

tb-profiler error report

• OS: linux
• Program version: 4.4.0
• Database version: c2fb9a2
• Program call:

  {'read1': './examp_seqs/SRR998657_1.fastq', 'read2': './examp_seqs/SRR998657_2.fastq', 'bam': None, 'fasta': None, 'vcf': None, 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'prefix': 'test.out', 'csv': False, 'txt': False, 'pdf': False, 'output_template': None, 'add_columns': None, 'add_mutation_metadata': False, 'dir': '.', 'mapper': 'bwa', 'caller': 'freebayes', 'calling_params': None, 'min_depth': 10, 'af': 0.1, 'reporting_af': 0.1, 'coverage_fraction_threshold': 0, 'missing_cov_threshold': 10, 'suspect': False, 'spoligotype': False, 'call_whole_genome': False, 'snp_dist': None, 'no_trim': False, 'no_flagstat': True, 'no_clip': True, 'no_delly': True, 'no_lineage': False, 'add_variant_annotations': False, 'threads': 1, 'ram': 2, 'verbose': 0, 'delly_vcf': None, 'no_clean': False, 'func': <function main_profile at 0x7fa4c4270310>, 'software_name': 'tbprofiler', 'tmp_prefix': '2da2cab3-503b-43f1-9e66-d42b2d2771ff', 'files_prefix': './2da2cab3-503b-43f1-9e66-d42b2d2771ff', 'conf': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'streptomycin', 'fluoroquinolones', 'moxifloxacin', 'ofloxacin', 'levofloxacin', 'ciprofloxacin', 'aminoglycosides', 'amikacin', 'capreomycin', 'kanamycin', 'cycloserine', 'ethionamide', 'clofazimine', 'para-aminosalicylic_acid', 'delamanid', 'bedaquiline', 'linezolid'], 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'version': 'tbdb.version.json', 'json_db': 'tbdb.dr.json', 'variables': 'tbdb.variables.json', 'spoligotype_spacers': 'tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': 'tbdb.spoligotype_list.csv', 'bedmask': 'tbdb.mask.bed', 'barcode': 'tbdb.barcode.bed'}, 'ref': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta', 'gff': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.gff', 'bed': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.bed', 'version': {'name': 'tbdb', 'commit': 'c2fb9a2', 'Author': 'jodyphelan <jody.phelan@lshtm.ac.uk>', 'Date': 'Tue Oct 4 11:40:15 2022 +0100'}, 'variables': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'streptomycin', 'fluoroquinolones', 'moxifloxacin', 'ofloxacin', 'levofloxacin', 'ciprofloxacin', 'aminoglycosides', 'amikacin', 'capreomycin', 'kanamycin', 'cycloserine', 'ethionamide', 'clofazimine', 'para-aminosalicylic_acid', 'delamanid', 'bedaquiline', 'linezolid'], 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'version': 'tbdb.version.json', 'json_db': 'tbdb.dr.json', 'variables': 'tbdb.variables.json', 'spoligotype_spacers': 'tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': 'tbdb.spoligotype_list.csv', 'bedmask': 'tbdb.mask.bed', 'barcode': 'tbdb.barcode.bed'}}, 'spoligotype_spacers': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.mask.bed', 'barcode': '/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.barcode.bed'}, 'run_delly': False, 'bam_file': './2da2cab3-503b-43f1-9e66-d42b2d2771ff.bam'}

  Traceback:

  File "/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/bin/tb-profiler", line 671, in <module>
  args.func(args)
  File "/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/bin/tb-profiler", line 151, in main_profile
  results.update(pp.run_profiler(args))
  File "/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/lib/python3.9/site-packages/pathogenprofiler/cli.py", line 37, in run_profiler
  results = bam_profiler(
  File "/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/lib/python3.9/site-packages/pathogenprofiler/profiler.py", line 30, in bam_profiler
  vcf_obj = bam_obj.call_variants(conf["ref"], caller=caller, bed_file=conf["bed"], threads=threads, calling_params=calling_params, samclip = samclip, min_dp=min_depth)
  File "/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/lib/python3.9/site-packages/pathogenprofiler/bam.py", line 82, in call_variants
  run_cmd('%(windows_cmd)s | parallel -j %(threads)s --col-sep " " "%(calling_cmd)s"' % vars(self))
  File "/home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/lib/python3.9/site-packages/pathogenprofiler/utils.py", line 409, in run_cmd
  raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,stderr.decode()))

  Value:

  Command Failed:
  set -u pipefail; cat /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.bed | awk '{print $1":"$2"-"$3" "$1"_"$2"_"$3}' | parallel -j 1 --col-sep " " "samtools view -T /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta -h ./2da2cab3-503b-43f1-9e66-d42b2d2771ff.bam {1} | samclip --ref /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta | samtools view -b > ./2da2cab3-503b-43f1-9e66-d42b2d2771ff.{2}.tmp.bam && samtools index ./2da2cab3-503b-43f1-9e66-d42b2d2771ff.{2}.tmp.bam && freebayes -f /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta -r {1} --haplotype-length -1  ./2da2cab3-503b-43f1-9e66-d42b2d2771ff.{2}.tmp.bam | bcftools view -c 1 | bcftools norm -f /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta | bcftools filter -t {1} -e 'FMT/DP<10' -S . -Oz -o ./2da2cab3-503b-43f1-9e66-d42b2d2771ff.{2}.vcf.gz"
  stderr:
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 583, removed 17, allowed 8, passed 566
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 655, removed 33, allowed 11, passed 622
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 291, removed 18, allowed 3, passed 273
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 297, removed 17, allowed 1, passed 280
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 239, removed 10, allowed 2, passed 229
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 818, removed 37, allowed 10, passed 781
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 854, removed 50, allowed 3, passed 804
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 674, removed 30, allowed 8, passed 644
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 204, removed 10, allowed 2, passed 194
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 192, removed 7, allowed 1, passed 185
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 169, removed 9, allowed 0, passed 160
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 215, removed 9, allowed 3, passed 206
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 476, removed 11, allowed 1, passed 465
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 203, removed 6, allowed 0, passed 197
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 313, removed 34, allowed 1, passed 279
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 197, removed 12, allowed 0, passed 185
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 549, removed 28, allowed 1, passed 521
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 929, removed 25, allowed 6, passed 904
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 240, removed 6, allowed 5, passed 234
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 318, removed 9, allowed 3, passed 309
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 336, removed 15, allowed 3, passed 321
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 193, removed 4, allowed 0, passed 189
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 302, removed 27, allowed 4, passed 275
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 578, removed 29, allowed 3, passed 549
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 793, removed 36, allowed 12, passed 757
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 492, removed 16, allowed 5, passed 476
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 383, removed 11, allowed 1, passed 372
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 363, removed 21, allowed 2, passed 342
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 283, removed 13, allowed 6, passed 270
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 236, removed 10, allowed 6, passed 226
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 321, removed 18, allowed 7, passed 303
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 292, removed 9, allowed 2, passed 283
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 183, removed 14, allowed 1, passed 169
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 371, removed 21, allowed 3, passed 350
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 200, removed 12, allowed 0, passed 188
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 266, removed 10, allowed 0, passed 256
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 338, removed 16, allowed 6, passed 322
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 151, removed 5, allowed 1, passed 146
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 395, removed 19, allowed 6, passed 376
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 322, removed 15, allowed 4, passed 307
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 148, removed 8, allowed 0, passed 140
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 325, removed 15, allowed 7, passed 310
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 269, removed 10, allowed 4, passed 259
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 330, removed 14, allowed 1, passed 316
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 330, removed 5, allowed 3, passed 325
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 316, removed 27, allowed 0, passed 289
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 181, removed 8, allowed 0, passed 173
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 552, removed 27, allowed 7, passed 525
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 167, removed 4, allowed 3, passed 163
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 631, removed 23, allowed 3, passed 608
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 605, removed 20, allowed 7, passed 585
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 679, removed 28, allowed 10, passed 651
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 408, removed 21, allowed 3, passed 387
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 241, removed 15, allowed 1, passed 226
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 925, removed 24, allowed 0, passed 901
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 206, removed 4, allowed 0, passed 202
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 171, removed 16, allowed 2, passed 155
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
  [samclip] Loading: /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Found 1 sequences in /home/n/noahlegall/.conda/envs/mbovpan_lite/envs/tb-profile/share/tbprofiler//tbdb.fasta.fai
  [samclip] Total SAM records 222, removed 8, allowed 3, passed 214
  [samclip] Header contained 20 lines
  [samclip] Done.
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type

[jodyphelan]

Hi @noahaus

Interesting, thanks for reporting the error. I wouldn't worry too much about the double slashes as this is permitted in path names. How did you download the read data? I can try on my side.

[noahaus]

@jodyphelan absolutely, I downloaded them using the SRA-toolkit fasterq-dump command. The accessions are SRR998656, SRR998657, SRR998658 and SRR998659. The command is as follows:

fasterq-dump SRR998656 -3

[noahaus]

If necessary, here is the conda YAML file if you would like to recreate that aswell

name: tb-profile
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - tb-profiler=4.4.0
  - python=3.9
  - ca-certificates
  - certifi
  - openssl

[noahaus]

Update:

I completely nuked my conda installation and started from scratch. I then redownloaded using mamba and recreated the environment with tb-profiler. I ran again, yet the problem remains. I'm starting to think maybe it is an issue with my HPC environment?

I also tried to use the quickstart command that is provided in the user docs, but the download is stalling for some reason and cannot download

[jodyphelan]

It seems to work ok for me, so I think you are right - it might be something specific to the server. Could you send me the explicit list of packages in your env with conda list --explicit > env.txt and upload the file here?

[noahaus]

Sure thing,

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
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https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/linux-64/freebayes-1.3.7-h1870644_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mamba-1.5.1-py310h51d5547_2.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/noarch/pathogen-profiler-3.0.0-pyh7cba7a3_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/noarch/tb-profiler-5.0.0-pyh7cba7a3_0.tar.bz2

[jodyphelan]

I've tested this with your environment and it seems the issue is the new version of freebayes. Downgrading to v1.3.6 should fix the issue:

mamba install freebayes=1.3.6

[noahaus]

Thank you Jody, it appears that has done the trick! I will close this issue, but I wanted to ask, is this behavior that occurs with every download of tb-profiler from conda? In the building of an environment, won't freebayes always download to the latest version?