ntm-profiler error report

OS: linux
ntm-profiler version: 0.2.0
pathogen-profiler version: 2.0.0
Database version: 93c979b

Program call:

{'no_clean': False, 'read1': 'Sample_R21113763-mix1-SM2.clean.read_1.fq.gz', 'read2': 'Sample_R21113763-mix1-SM2.clean.read_2.fq.gz', 'bam': None, 'fasta': None, 'vcf': None, 'platform': 'illumina', 'resistance_db': None, 'external_resistance_db': None, 'species_db': 'ntmdb', 'external_species_db': None, 'prefix': 'my_test', 'dir': '.', 'csv': False, 'txt': False, 'add_columns': None, 'add_mutation_metadata': False, 'call_whole_genome': False, '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, 'species_only': False, 'no_trim': False, 'no_flagstat': False, 'no_clip': True, 'no_delly': False, 'no_species': False, 'no_mash': False, 'output_kmer_counts': 'my_test.kmers.txt', 'add_variant_annotations': False, 'threads': 1, 'verbose': 0, 'no_cleanup': False, 'delly_vcf': None, 'func': <function main_profile at 0x7f42f1fcc310>, 'software_name': 'ntm-profiler', 'tmp_prefix': '6468baa2-af8e-4517-b20e-a1ef79bfdba2', 'files_prefix': './6468baa2-af8e-4517-b20e-a1ef79bfdba2', 'conf': {'snpEff_db': 'Mycobacterium_abscessus_atcc_19977', 'species': ['Mycobacterium abscessus subsp. abscessus', 'Mycobacterium abscessus subsp. bolletii', 'Mycobacterium abscessus subsp. massiliense'], 'drugs': ['macrolides', 'amikacin'], 'amplicon': False, 'files': {'ref': 'Mycobacterium_abscessus_subsp._abscessus.fasta', 'gff': 'Mycobacterium_abscessus_subsp._abscessus.gff', 'bed': 'Mycobacterium_abscessus_subsp._abscessus.bed', 'version': 'Mycobacterium_abscessus_subsp._abscessus.version.json', 'json_db': 'Mycobacterium_abscessus_subsp._abscessus.dr.json', 'variables': 'Mycobacterium_abscessus_subsp._abscessus.variables.json'}, 'ref': '/home/seq/anaconda3/envs/ntm/share/ntm-profiler//Mycobacterium_abscessus_subsp._abscessus.fasta', 'gff': '/home/seq/anaconda3/envs/ntm/share/ntm-profiler//Mycobacterium_abscessus_subsp._abscessus.gff', 'bed': '/home/seq/anaconda3/envs/ntm/share/ntm-profiler//Mycobacterium_abscessus_subsp._abscessus.bed', 'version': {'name': 'Mycobacterium_abscessus_subsp._abscessus', 'commit': '93c979b', 'Merge': '36da4bf 8294c47', 'Author': 'Jody Phelan <jody.phelan@lshtm.ac.uk>', 'Date': 'Fri Apr 29 17:33:42 2022 +0100'}, 'json_db': {'MAB_r5052': {'n.2270A>C': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466477], 'chromosome': 'CU458896'}, 'n.2270A>G': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466477], 'chromosome': 'CU458896'}, 'n.2270A>T': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466477], 'chromosome': 'CU458896'}, 'n.2271A>C': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466478], 'chromosome': 'CU458896'}, 'n.2271A>G': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466478], 'chromosome': 'CU458896'}, 'n.2271A>T': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466478], 'chromosome': 'CU458896'}, 'n.2281G>A': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466488], 'chromosome': 'CU458896'}, 'n.2281G>C': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466488], 'chromosome': 'CU458896'}, 'n.2281G>T': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466488], 'chromosome': 'CU458896'}, 'n.2293A>C': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466500], 'chromosome': 'CU458896'}, 'n.2293A>G': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466500], 'chromosome': 'CU458896'}, 'n.2293A>T': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1466500], 'chromosome': 'CU458896'}}, 'MAB_r5051': {'n.1374A>G': {'annotations': [{'type': 'drug', 'drug': 'amikacin', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1463771], 'chromosome': 'CU458896'}, 'n.1374A>C': {'annotations': [{'type': 'drug', 'drug': 'amikacin', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1463771], 'chromosome': 'CU458896'}, 'n.1374A>T': {'annotations': [{'type': 'drug', 'drug': 'amikacin', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': [1463771], 'chromosome': 'CU458896'}, 'n.1375A>C': {'annotations': [{'type': 'drug', 'drug': 'amikacin', 'confers': 'resistance'}], 'genome_positions': [1463772], 'chromosome': 'CU458896'}, 'n.1375A>G': {'annotations': [{'type': 'drug', 'drug': 'amikacin', 'confers': 'resistance'}], 'genome_positions': [1463772], 'chromosome': 'CU458896'}, 'n.1375A>T': {'annotations': [{'type': 'drug', 'drug': 'amikacin', 'confers': 'resistance'}], 'genome_positions': [1463772], 'chromosome': 'CU458896'}}, 'MAB_2297': {'frameshift': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'sensitivity', 'interaction': 'Override=MAB_2297:functional_gene', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': None, 'chromosome': 'CU458896'}, 'large_deletion': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'sensitivity', 'interaction': 'Override=MAB_2297:functional_gene', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': None, 'chromosome': 'CU458896'}, 'p.Trp10Arg': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'sensitivity', 'interaction': 'Override=MAB_2297:functional_gene', 'literature': '10.1128/JCM.02950-14'}], 'genome_positions': [2345982, 2345983, 2345984], 'chromosome': 'CU458896'}, 'functional_gene': {'annotations': [{'type': 'drug', 'drug': 'macrolides', 'confers': 'resistance', 'literature': '10.1038/s41467-021-25484-9'}], 'genome_positions': None, 'chromosome': 'CU458896'}}}, 'variables': {'snpEff_db': 'Mycobacterium_abscessus_atcc_19977', 'species': ['Mycobacterium abscessus subsp. abscessus', 'Mycobacterium abscessus subsp. bolletii', 'Mycobacterium abscessus subsp. massiliense'], 'drugs': ['macrolides', 'amikacin'], 'amplicon': False, 'files': {'ref': 'Mycobacterium_abscessus_subsp._abscessus.fasta', 'gff': 'Mycobacterium_abscessus_subsp._abscessus.gff', 'bed': 'Mycobacterium_abscessus_subsp._abscessus.bed', 'version': 'Mycobacterium_abscessus_subsp._abscessus.version.json', 'json_db': 'Mycobacterium_abscessus_subsp._abscessus.dr.json', 'variables': 'Mycobacterium_abscessus_subsp._abscessus.variables.json'}}}, 'run_delly': True, 'bam_file': './6468baa2-af8e-4517-b20e-a1ef79bfdba2.bam'}

Traceback:

File "/home/seq/anaconda3/envs/ntm/bin/ntm-profiler", line 322, in <module>
args.func(args)
File "/home/seq/anaconda3/envs/ntm/bin/ntm-profiler", line 120, in main_profile
results.update(pp.run_profiler(args))
File "/home/seq/anaconda3/envs/ntm/lib/python3.8/site-packages/pathogenprofiler/cli.py", line 37, in run_profiler
results = bam_profiler(
File "/home/seq/anaconda3/envs/ntm/lib/python3.8/site-packages/pathogenprofiler/profiler.py", line 42, in bam_profiler
bam_obj.flagstat()
File "/home/seq/anaconda3/envs/ntm/lib/python3.8/site-packages/pathogenprofiler/bam.py", line 89, in flagstat
run_cmd(f"samtools flagstat -O json {self.bam_file} > {tmpfile}")
File "/home/seq/anaconda3/envs/ntm/lib/python3.8/site-packages/pathogenprofiler/utils.py", line 391, in run_cmd
raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,stderr.decode()))

Value:

Command Failed:
set -u pipefail; samtools flagstat -O json ./6468baa2-af8e-4517-b20e-a1ef79bfdba2.bam > 81de7f71-41c3-4a48-84bc-422ad23838f4
stderr:
flagstat: invalid option -- 'O'
Usage: samtools flagstat [options] <in.bam>
  --input-fmt-option OPT[=VAL]
           Specify a single input file format option in the form
           of OPTION or OPTION=VALUE
-@, --threads INT
           Number of additional threads to use [0]

jodyphelan / NTM-Profiler

I got this error when I tried to run the analysis of fastq data. #26

ntm-profiler error report

Traceback:

Value: