jodyphelan
commented
2 months ago 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.
Open BhawnaY16 opened 2 months ago
jodyphelan
commented
2 months ago 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
commented
2 months ago 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
commented
2 months ago 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?
{'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 <jody.phelan@lshtm.ac.uk>', '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 <jody.phelan@lshtm.ac.uk>', '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}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()))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'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
commented
2 months ago #
_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}" --csvdone
BhawnaY16
commented
2 months ago 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
commented
2 months ago 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
{'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 <jody.phelan@lshtm.ac.uk>', '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 <jody.phelan@lshtm.ac.uk>', '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}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()))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
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
Traceback:
Value: