TB-PROFILER RUN ISSUE

[BhawnaY16]

Hey,
I was trying to run the tb-profiler on my samples.I am facing this delly issue.Can you please look into it?

tb-profiler error report

• OS: linux
• Program version: 6.2.1
• Database version: {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan [email protected]', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}
• Program call:

{'logging': 'INFO', 'read1': '2400139177_2024_S17_R1_001.fastq.gz', 'read2': '2400139177_2024_S17_R2_001.fastq.gz', 'bam': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c.bam', 'fasta': None, 'vcf': None, 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'prefix': '2400139177_2024_S17', 'csv': True, 'txt': False, 'text_template': None, 'docx': False, 'docx_template': None, 'add_columns': None, 'add_mutation_metadata': False, 'dir': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results', 'depth': '0,10', 'af': '0,0.1', 'strand': '0,3', 'sv_depth': '0,10', 'sv_af': '0.5,0.9', 'sv_len': '100000,50000', 'mapper': 'bwa', 'caller': 'freebayes', 'calling_params': None, 'kmer_counter': 'kmc', 'coverage_tool': 'samtools', 'suspect': False, 'spoligotype': False, 'update_phylo': False, 'call_whole_genome': False, 'snp_dist': None, 'snp_diff_db': None, 'snp_diff_no_store': False, 'no_trim': False, 'no_coverage_qc': False, 'no_samclip': False, 'no_delly': False, 'no_lineage': False, 'add_variant_annotations': False, 'threads': 96, 'ram': 2, 'delly_vcf': None, 'supplementary_bam': None, 'no_clean': False, 'temp': '.', 'func': <function main_profile at 0x7f2101a17560>, 'software_name': 'tbprofiler', 'version': '6.2.1', 'tmp_prefix': '434deb43-00ec-473c-bdd9-f6784fc4876c', 'files_prefix': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c', 'conf': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', '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', 'rules': 'tbdb.rules.txt'}, 'ref': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.fasta', 'gff': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.gff', 'bed': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.bed', 'variables': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', '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', 'rules': 'tbdb.rules.txt'}}, 'spoligotype_spacers': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.mask.bed', 'barcode': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.barcode.bed', 'rules': ['Variant(gene_name=mmpL5,type=lof) inactivates_resistance Variant(gene_name=mmpR5)', 'Variant(gene_name=eis,type=lof) inactivates_resistance Variant(gene_name=eis)'], 'variant_filters': {'depth_hard': 0, 'depth_soft': 10, 'af_hard': 0, 'af_soft': 0.1, 'strand_hard': 0, 'strand_soft': 3, 'sv_depth_hard': 0, 'sv_depth_soft': 10, 'sv_af_hard': 0.5, 'sv_af_soft': 0.9, 'sv_len_hard': 100000, 'sv_len_soft': 50000}}, 'run_delly': True, 'samclip': True, 'coverage_qc': True, 'data_source': 'fastq', 'call_lineage': True}

Traceback:

  File "/home/user/miniconda3/envs/tbprofiler-env/bin/tb-profiler", line 587, in <module>
    args.func(args)
  File "/home/user/miniconda3/envs/tbprofiler-env/bin/tb-profiler", line 101, in main_profile
    variants_profile = pp.run_profiler(args)
                       ^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 192, in run_profiler
    get_vcf_file(args)
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 174, in get_vcf_file
    args.vcf = get_vcf_from_bam(args)
               ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 154, in get_vcf_from_bam
    delly_vcf_obj = bam.run_delly(conf['bed'])
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/bam.py", line 91, in run_delly
    run_cmd("delly call -t DEL -g %(ref_file)s %(bam_file)s -o %(prefix)s.delly.bcf" % vars(self))
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/utils.py", line 486, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))

Value:

Command Failed:
/bin/bash -c set -o pipefail; delly call -t DEL -g /home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.fasta /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c.bam -o /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c.delly.bcf
stderr:
[2024-Jul-09 15:12:15] delly call -t DEL -g /home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.fasta /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c.bam -o /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c.delly.bcf 
Sample has not enough data to estimate library parameters! File: /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/434deb43-00ec-473c-bdd9-f6784fc4876c.bam

[jodyphelan]

It probably means there is very little data available in your sample. I will make a patch where it will stop the pipeline from exiting.

[BhawnaY16]

I have run the pipeline on same data and it worked successfully before.I was trying to reproduce the results and I got this error.

[BhawnaY16]

Hey! I have tried running the pipeline on open source data available too, just to check if it is sample issue. But the pipeline is still throwing error. Can you look into it?

tb-profiler error report

• OS: linux
• Program version: 6.2.1
• Database version: {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan [email protected]', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}
• Program call:

{'logging': 'INFO', 'read1': 'ERR10679991_1.fastq.gz', 'read2': 'ERR10679991_2.fastq.gz', 'bam': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new/e67233f6-54df-4d47-ab14-5f04e14826f8.bam', 'fasta': None, 'vcf': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new/e67233f6-54df-4d47-ab14-5f04e14826f8.targets.vcf.gz', 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'prefix': 'ERR10679991', 'csv': True, 'txt': False, 'text_template': None, 'docx': False, 'docx_template': None, 'add_columns': None, 'add_mutation_metadata': False, 'dir': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new', 'depth': '0,10', 'af': '0,0.1', 'strand': '0,3', 'sv_depth': '0,10', 'sv_af': '0.5,0.9', 'sv_len': '100000,50000', 'mapper': 'bwa', 'caller': 'freebayes', 'calling_params': None, 'kmer_counter': 'kmc', 'coverage_tool': 'samtools', 'suspect': False, 'spoligotype': False, 'update_phylo': False, 'call_whole_genome': False, 'snp_dist': None, 'snp_diff_db': None, 'snp_diff_no_store': False, 'no_trim': False, 'no_coverage_qc': False, 'no_samclip': False, 'no_delly': False, 'no_lineage': False, 'add_variant_annotations': False, 'threads': 96, 'ram': 2, 'delly_vcf': None, 'supplementary_bam': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new/e67233f6-54df-4d47-ab14-5f04e14826f8.bam', 'no_clean': False, 'temp': '.', 'func': <function main_profile at 0x7f407ec5b4c0>, 'software_name': 'tbprofiler', 'version': '6.2.1', 'tmp_prefix': 'e67233f6-54df-4d47-ab14-5f04e14826f8', 'files_prefix': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new/e67233f6-54df-4d47-ab14-5f04e14826f8', 'conf': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', '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', 'rules': 'tbdb.rules.txt'}, 'ref': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.fasta', 'gff': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.gff', 'bed': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.bed', 'variables': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', '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', 'rules': 'tbdb.rules.txt'}}, 'spoligotype_spacers': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.mask.bed', 'barcode': '/home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.barcode.bed', 'rules': ['Variant(gene_name=mmpL5,type=lof) inactivates_resistance Variant(gene_name=mmpR5)', 'Variant(gene_name=eis,type=lof) inactivates_resistance Variant(gene_name=eis)'], 'variant_filters': {'depth_hard': 0, 'depth_soft': 10, 'af_hard': 0, 'af_soft': 0.1, 'strand_hard': 0, 'strand_soft': 3, 'sv_depth_hard': 0, 'sv_depth_soft': 10, 'sv_af_hard': 0.5, 'sv_af_soft': 0.9, 'sv_len_hard': 100000, 'sv_len_soft': 50000}}, 'run_delly': True, 'samclip': True, 'coverage_qc': True, 'data_source': 'fastq', 'call_lineage': True}

Traceback:

  File "/home/user/miniconda3/envs/tbprofiler-env/bin/tb-profiler", line 587, in <module>
    args.func(args)
  File "/home/user/miniconda3/envs/tbprofiler-env/bin/tb-profiler", line 101, in main_profile
    variants_profile = pp.run_profiler(args)
                       ^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 204, in run_profiler
    annotated_variants = vcf_profiler(args)
                         ^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/profiler.py", line 47, in vcf_profiler
    annotated_variants = vcf_variant_profiler(conf, args.files_prefix, args.vcf, bam_for_phasing=args.supplementary_bam)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/profiler.py", line 61, in vcf_variant_profiler
    vcf_obj = vcf_obj.run_snpeff(conf["snpEff_db"],conf["ref"],conf["gff"],rename_chroms= conf.get("chromosome_conversion",None),bam_for_phasing=bam_for_phasing)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/vcf.py", line 138, 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 %(phasing_bam)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/user/miniconda3/envs/tbprofiler-env/lib/python3.12/site-packages/pathogenprofiler/utils.py", line 486, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))

Value:

Command Failed:
/bin/bash -c set -o pipefail; bcftools view -c 1 -a /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new/e67233f6-54df-4d47-ab14-5f04e14826f8.targets_for_profile.vcf.gz | bcftools view -v snps | combine_vcf_variants.py --ref /home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.fasta --gff /home/user/miniconda3/envs/tbprofiler-env/share/tbprofiler//tbdb.gff --bam /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/tb-profiler/new/e67233f6-54df-4d47-ab14-5f04e14826f8.bam |  snpEff ann -dataDir /home/user/miniconda3/envs/tbprofiler-env/share/snpeff-5.2-1/data -noLog -noStats Mycobacterium_tuberculosis_h37rv -  | bcftools sort -Oz -o 0385f5e9-d000-4191-bc1d-a36ed7607561.1.vcf.gz && bcftools index 0385f5e9-d000-4191-bc1d-a36ed7607561.1.vcf.gz
stderr:
Writing to /tmp/bcftools-sort.GQmvJi
  File "/home/user/miniconda3/envs/tbprofiler-env/bin/snpEff", line 108
    sys.exit(print(java_args))
                 ^
SyntaxError: invalid syntax
[E::bcf_hdr_read] Input is not detected as bcf or vcf format
Could not read VCF/BCF headers from -
Cleaning
Traceback (most recent call last):
  File "/home/user/miniconda3/envs/tbprofiler-env/bin/combine_vcf_variants.py", line 185, in <module>
    new_vcf.write(var)
  File "pysam/libcbcf.pyx", line 4482, in pysam.libcbcf.VariantFile.write
  File "pysam/libcbcf.pyx", line 4519, in pysam.libcbcf.VariantFile.write
BrokenPipeError: [Errno 32] b'Broken pipe'

[jodyphelan]

Thanks, this looks like a different error. Would you be able to attach the output of conda list here? And could you give me the command you are using?

[BhawnaY16]

packages in environment at /home/user/miniconda3/envs/tbprofiler-env:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
bcftools 1.20 h8b25389_0 bioconda
bedtools 2.31.1 hf5e1c6e_1 bioconda
bitstring 3.1.9 pyhd8ed1ab_0 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py312h30efb56_1 conda-forge
bwa 0.7.18 he4a0461_0 bioconda
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
cachetools 4.2.4 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2024.6.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py312hf06ca03_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cmake 3.29.4 h91dbaaa_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py312h8572e83_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
delly 1.1.6 h6b1aa3f_2 bioconda
deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
docxtpl 0.11.5 pyhd8ed1ab_0 conda-forge
dsk 2.3.3 h43eeafb_4 bioconda
eigen 3.2 3 bioconda
expat 2.6.2 h59595ed_0 conda-forge
filelock 3.15.4 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_2 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.53.0 py312h9a8786e_0 conda-forge
freebayes 1.3.6 hb0f3ef8_7 bioconda
freetype 2.12.1 h267a509_2 conda-forge
gatk4 4.5.0.0 py36hdfd78af_0 bioconda
gawk 5.3.0 ha916aea_0 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
git 2.45.1 pl5321hef9f9f3_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gsl 2.7 he838d99_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
harfbuzz 8.5.0 hfac3d4d_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
htslib 1.20 h5efdd21_1 bioconda
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
iqtree 2.3.4 hdcf5f25_2 bioconda
isa-l 2.31.0 hd590300_1 conda-forge
itol-config 0.1.0 pyhdfd78af_0 bioconda
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
jsoncpp 1.9.5 h4bd325d_1 conda-forge
k8 0.2.5 hdcf5f25_4 bioconda
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py312h8572e83_1 conda-forge
kmc 3.2.4 h6dccd9a_1 bioconda
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libcbor 0.10.2 hcb278e6_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libfido2 1.14.0 h4446dcb_0 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 14.1.0 h69a702a_0 conda-forge
libgfortran5 14.1.0 hc5f4f2c_0 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libgomp 14.1.0 h77fa898_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libudev1 255 h3f72095_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.48.0 hd590300_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 hc051c1a_1 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
lofreq 2.1.5 py312he57d009_12 bioconda
lxml 5.2.2 py312hb90d8a5_0 conda-forge
mafft 7.525 h031d066_1 bioconda
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py312h98912ed_0 conda-forge
matplotlib-base 3.9.0 py312h9201f00_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
minimap2 2.28 he4a0461_1 bioconda
mpfr 4.2.1 h9458935_1 conda-forge
mpi 1.0 openmpi conda-forge
munkres 1.0.7 py_1 bioconda
mysql-connector-c 6.1.11 h659d440_1008 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
numpy 2.0.0 py312h22e1c76_0 conda-forge
openjdk 17.0.11 h24d6bf4_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openmpi 4.1.2 hbfc84c5_0 conda-forge
openssh 9.6p1 h2d3b35a_0 conda-forge
openssl 3.3.1 h4ab18f5_1 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
parallel 20170422 pl5.22.0_0 bioconda
pathogen-profiler 4.2.0 pyh7e72e81_1 bioconda
pcre2 10.43 hcad00b1_0 conda-forge
perl 5.22.0.1 0 conda-forge
pillow 10.3.0 py312hdcec9eb_0 conda-forge
pilon 1.24 hdfd78af_0 bioconda
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 2.8.0 pyhd8ed1ab_0 conda-forge
pydantic-core 2.20.0 py312h4413252_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysam 0.22.1 py312hcfdcdd7_1 bioconda
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.3 hab00c5b_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-docx 1.1.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
qhull 2020.2 h4bd325d_2 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rhash 1.4.4 hd590300_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
rich-argparse 1.5.2 pyhd8ed1ab_0 conda-forge
samclip 0.4.0 hdfd78af_1 bioconda
samtools 1.20 h50ea8bc_0 bioconda
scipy 1.14.0 py312hc2bc53b_0 conda-forge
screed 1.1.3 pyhd8ed1ab_0 conda-forge
seqkit 2.8.2 h9ee0642_0 bioconda
setuptools 70.1.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snpeff 5.2 hdfd78af_1 bioconda
sourmash 4.8.10 hdfd78af_0 bioconda
sourmash-minimal 4.8.10 py312h5a5b059_0 conda-forge
tabixpp 1.1.2 h27d5293_2 bioconda
tb-profiler 6.2.1 pyhdfd78af_0 bioconda
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tqdm 4.66.4 pyhd8ed1ab_0 conda-forge
trimmomatic 0.39 hdfd78af_2 bioconda
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
ucsc-fatovcf 448 h2a80c09_1 bioconda
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
usher 0.6.3 hb389108_1 bioconda
vcflib 1.0.9 hdcf5f25_6 bioconda
wfa2-lib 2.3.5 h4ac6f70_0 bioconda
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.22.0 py312h5b18bf6_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge

Command used-

for file in *_1.fastq.gz; do

sample_name=$(basename "$file" _1.fastq.gz)


tb-profiler profile -1 "${sample_name}_1.fastq.gz" -2 "${sample_name}_2.fastq.gz" -t 96 -p "${sample_name}" --csv

done

[BhawnaY16]

Hey!
Since you have update the tb-profiler version, bioconda doesn't seem to have the latest version. It will be helpful if you can share the version of dependencies you have used as I am trying to manually install it and I am facing conflict issues.
Thanks!

[BhawnaY16]

I'm trying to run the v6.2.1 on my data sets. I am using amplicon data but I get keep encountering the error. Coverage of my samples is good. Is there some way to handle the amplicon data. I have changed the option amplicon=true and provided amplicon primer file path too. Can you please help

tb-profiler error report

• OS: linux
• Program version: 6.2.1
• Database version: {'name': 'tbdb', 'commit': '72ef6fa', 'Author': 'Jody Phelan [email protected]', 'Date': 'Tue Jul 16 16:56:19 2024 +0100'}
• Program call:

{'logging': 'INFO', 'read1': '2400139177_2024_S17_R1_001.fastq.gz', 'read2': '2400139177_2024_S17_R2_001.fastq.gz', 'bam': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05.bam', 'fasta': None, 'vcf': None, 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'prefix': '2400139177_2024_S17', 'csv': True, 'txt': False, 'text_template': None, 'docx': False, 'docx_template': None, 'add_columns': None, 'add_mutation_metadata': False, 'dir': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results', 'depth': '0,10', 'af': '0,0.1', 'strand': '0,3', 'sv_depth': '0,10', 'sv_af': '0.5,0.9', 'sv_len': '100000,50000', 'mapper': 'bwa', 'caller': 'freebayes', 'calling_params': None, 'kmer_counter': 'kmc', 'coverage_tool': 'samtools', 'suspect': False, 'spoligotype': False, 'update_phylo': False, 'call_whole_genome': False, 'snp_dist': None, 'snp_diff_db': None, 'snp_diff_no_store': False, 'no_trim': False, 'no_coverage_qc': False, 'no_samclip': False, 'no_delly': False, 'no_lineage': False, 'add_variant_annotations': False, 'threads': 96, 'ram': 2, 'delly_vcf': None, 'supplementary_bam': None, 'no_clean': False, 'temp': '.', 'func': <function main_profile at 0x7f26ada7ee60>, 'software_name': 'tbprofiler', 'version': '6.2.1', 'tmp_prefix': '427b5cf7-85d2-4088-9c1d-d565b3a09b05', 'files_prefix': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05', 'conf': {'db-schema-version': '1.0.0', 'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '72ef6fa', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Tue Jul 16 16:56:19 2024 +0100'}, 'amplicon': True, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', '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', 'rules': 'tbdb.rules.txt', 'amplicon_primers': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/tb.txt'}, 'ref': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.fasta', 'gff': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.gff', 'bed': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.bed', 'variables': {'db-schema-version': '1.0.0', 'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '72ef6fa', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Tue Jul 16 16:56:19 2024 +0100'}, 'amplicon': True, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', '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', 'rules': 'tbdb.rules.txt', 'amplicon_primers': '/media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/tb.txt'}}, 'spoligotype_spacers': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.mask.bed', 'barcode': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.barcode.bed', 'rules': ['Variant(gene_name=mmpL5,type=lof) inactivates_resistance Variant(gene_name=mmpR5)', 'Variant(gene_name=eis,type=lof) inactivates_resistance Variant(gene_name=eis)'], 'amplicon_primers': '/home/user/miniconda3/envs/tb-profiler/share/tbprofiler///media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/tb.txt', 'variant_filters': {'depth_hard': 0, 'depth_soft': 10, 'af_hard': 0, 'af_soft': 0.1, 'strand_hard': 0, 'strand_soft': 3, 'sv_depth_hard': 0, 'sv_depth_soft': 10, 'sv_af_hard': 0.5, 'sv_af_soft': 0.9, 'sv_len_hard': 100000, 'sv_len_soft': 50000}}, 'run_delly': True, 'samclip': True, 'coverage_qc': True, 'data_source': 'fastq', 'call_lineage': True}

Traceback:

  File "/home/user/miniconda3/envs/tb-profiler/bin/tb-profiler", line 587, in <module>
    args.func(args)
  File "/home/user/miniconda3/envs/tb-profiler/bin/tb-profiler", line 101, in main_profile
    variants_profile = pp.run_profiler(args)
  File "/home/user/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/cli.py", line 192, in run_profiler
    get_vcf_file(args)
  File "/home/user/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/cli.py", line 174, in get_vcf_file
    args.vcf = get_vcf_from_bam(args)
  File "/home/user/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/cli.py", line 154, in get_vcf_from_bam
    delly_vcf_obj = bam.run_delly(conf['bed'])
  File "/home/user/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/bam.py", line 91, in run_delly
    run_cmd("delly call -t DEL -g %(ref_file)s %(bam_file)s -o %(prefix)s.delly.bcf" % vars(self))
  File "/home/user/miniconda3/envs/tb-profiler/lib/python3.10/site-packages/pathogenprofiler/utils.py", line 486, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))

Value:

Command Failed:
/bin/bash -c set -o pipefail; delly call -t DEL -g /home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.fasta /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05.bam -o /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05.delly.bcf
stderr:
[2024-Jul-18 14:30:05] delly call -t DEL -g /home/user/miniconda3/envs/tb-profiler/share/tbprofiler//tbdb.fasta /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05.bam -o /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05.delly.bcf 
Sample has not enough data to estimate library parameters! File: /media/user/36d81ee3-f383-4bc4-b619-20abd785be33/DATA/26.06.2024/sngenelab_cordon_pool3_2024-06-24_1446/POOL3/trimmed_results/427b5cf7-85d2-4088-9c1d-d565b3a09b05.bam