[2024-01-24 12:13:57,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:57,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:57,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference
[2024-01-24 12:13:58,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:58,884] [INFO] Task started: Prodigal
[2024-01-24 12:13:58,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a95a5a5-e4be-41d8-9b74-b81b27ada279/GCF_002104675.1_ASM210467v1_genomic.fna.gz | prodigal -d GCF_002104675.1_ASM210467v1_genomic.fna/cds.fna -a GCF_002104675.1_ASM210467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:17,100] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:17,101] [INFO] Task started: HMMsearch
[2024-01-24 12:14:17,101] [INFO] Running command: hmmsearch --tblout GCF_002104675.1_ASM210467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference/reference_markers.hmm GCF_002104675.1_ASM210467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:17,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:17,454] [INFO] Found 6/6 markers.
[2024-01-24 12:14:17,502] [INFO] Query marker FASTA was written to GCF_002104675.1_ASM210467v1_genomic.fna/markers.fasta
[2024-01-24 12:14:17,502] [INFO] Task started: Blastn
[2024-01-24 12:14:17,502] [INFO] Running command: blastn -query GCF_002104675.1_ASM210467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference/reference_markers.fasta -out GCF_002104675.1_ASM210467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:18,573] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:18,577] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:18,577] [INFO] Target genome list was writen to GCF_002104675.1_ASM210467v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:18,586] [INFO] Task started: fastANI
[2024-01-24 12:14:18,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a95a5a5-e4be-41d8-9b74-b81b27ada279/GCF_002104675.1_ASM210467v1_genomic.fna.gz --refList GCF_002104675.1_ASM210467v1_genomic.fna/target_genomes.txt --output GCF_002104675.1_ASM210467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:52,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:52,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:52,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:52,601] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:52,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:52,602] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mycobacterium tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	85.8285	1112	1688	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	85.8211	1051	1688	95	below_threshold
Mycobacterium tuberculosis variant pinnipedii	strain=ATCC BAA-688	GCA_002982275.1	194542	1773	type	True	85.749	1126	1688	95	below_threshold
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	85.7472	1119	1688	95	below_threshold
Mycobacterium tuberculosis variant bovis	strain=ATCC 19210	GCA_002982285.1	1765	1773	type	True	85.7228	1020	1688	95	below_threshold
Mycobacterium tuberculosis variant caprae	strain=ATCC BAA-824	GCA_002982225.1	115862	1773	type	True	85.7225	1124	1688	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	85.7221	1145	1688	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	85.6661	1157	1688	95	below_threshold
Mycobacterium gastri	strain=DSM 43505	GCA_002102175.1	1777	1777	type	True	81.5088	1073	1688	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	81.3552	1101	1688	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	81.308	1058	1688	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.2616	1018	1688	95	below_threshold
Mycobacterium kansasii	strain=ATCC 12478	GCA_000157895.2	1768	1768	type	True	81.1446	1117	1688	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	80.8518	972	1688	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	80.8379	883	1688	95	below_threshold
Mycobacterium attenuatum	strain=MK41	GCA_900566085.1	2341086	2341086	type	True	80.8092	1039	1688	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	80.5393	863	1688	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.536	927	1688	95	below_threshold
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_001515365.1	265949	265949	suspected-type	True	80.2132	997	1688	95	below_threshold
Mycobacterium basiliense		GCA_900292015.1	2094119	2094119	type	True	80.2043	1046	1688	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	80.0886	984	1688	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	80.0241	1007	1688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:52,603] [INFO] DFAST Taxonomy check result was written to GCF_002104675.1_ASM210467v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:52,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:52,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:52,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference/checkm_data
[2024-01-24 12:14:52,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:52,657] [INFO] Task started: CheckM
[2024-01-24 12:14:52,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104675.1_ASM210467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104675.1_ASM210467v1_genomic.fna/checkm_input GCF_002104675.1_ASM210467v1_genomic.fna/checkm_result
[2024-01-24 12:15:42,813] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:42,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,842] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:42,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:42,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104675.1_ASM210467v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:42,843] [INFO] Task started: Blastn
[2024-01-24 12:15:42,844] [INFO] Running command: blastn -query GCF_002104675.1_ASM210467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg386034a5-16b2-4a4b-966e-2032296dcdb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104675.1_ASM210467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:44,326] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:44,330] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:44,330] [INFO] Target genome list was writen to GCF_002104675.1_ASM210467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:44,346] [INFO] Task started: fastANI
[2024-01-24 12:15:44,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a95a5a5-e4be-41d8-9b74-b81b27ada279/GCF_002104675.1_ASM210467v1_genomic.fna.gz --refList GCF_002104675.1_ASM210467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104675.1_ASM210467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:09,799] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:09,821] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:09,822] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002104675.1	s__Mycobacterium decipiens	100.0	1682	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000195955.2	s__Mycobacterium tuberculosis	85.6678	1157	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_010731535.1	s__Mycobacterium lacus	82.7173	1154	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010730055.1	s__Mycobacterium shinjukuense	82.5518	1040	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900232995.1	s__Mycobacterium simulans	81.7538	1188	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_900566055.1	s__Mycobacterium innocens	81.5157	1069	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002102175.1	s__Mycobacterium gastri	81.5154	1072	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.95	99.95	0.95	0.95	2	-
GCF_001954275.1	s__Mycobacterium sp001954275	81.3814	959	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.3408	1103	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002086675.1	s__Mycobacterium persicum	81.3246	1057	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_002101815.1	s__Mycobacterium paraense	81.2848	1014	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001954195.1	s__Mycobacterium sp001954195	81.2623	965	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCA_002102225.1	s__Mycobacterium interjectum_B	81.252	1008	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.197	974	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	81.1422	974	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157895.3	s__Mycobacterium kansasii	81.1203	1122	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.15	0.98	0.95	35	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	81.0776	1126	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002116635.1	s__Mycobacterium szulgai	80.9955	1093	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566085.1	s__Mycobacterium attenuatum	80.8122	1039	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.59	99.54	0.94	0.93	4	-
GCF_900292015.1	s__Mycobacterium basiliense	80.2084	1044	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.0884	982	1688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:09,823] [INFO] GTDB search result was written to GCF_002104675.1_ASM210467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:09,824] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:09,829] [INFO] DFAST_QC result json was written to GCF_002104675.1_ASM210467v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:09,830] [INFO] DFAST_QC completed!
[2024-01-24 12:16:09,830] [INFO] Total running time: 0h2m12s