[2024-01-24 10:47:09,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,927] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgba243f6e-397f-491f-830e-a5fdae00a935/GCF_025822345.1_ASM2582234v1_genomic.fna.gz | prodigal -d GCF_025822345.1_ASM2582234v1_genomic.fna/cds.fna -a GCF_025822345.1_ASM2582234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:34,990] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:34,991] [INFO] Task started: HMMsearch
[2024-01-24 10:47:34,991] [INFO] Running command: hmmsearch --tblout GCF_025822345.1_ASM2582234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference/reference_markers.hmm GCF_025822345.1_ASM2582234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,346] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,404] [INFO] Query marker FASTA was written to GCF_025822345.1_ASM2582234v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,404] [INFO] Task started: Blastn
[2024-01-24 10:47:35,404] [INFO] Running command: blastn -query GCF_025822345.1_ASM2582234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference/reference_markers.fasta -out GCF_025822345.1_ASM2582234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,667] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,672] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:36,672] [INFO] Target genome list was writen to GCF_025822345.1_ASM2582234v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:37,329] [INFO] Task started: fastANI
[2024-01-24 10:47:37,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgba243f6e-397f-491f-830e-a5fdae00a935/GCF_025822345.1_ASM2582234v1_genomic.fna.gz --refList GCF_025822345.1_ASM2582234v1_genomic.fna/target_genomes.txt --output GCF_025822345.1_ASM2582234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:02,968] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:02,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:02,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:02,987] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:02,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:02,988] [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
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	99.9861	2173	2219	95	conclusive
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	99.9779	2168	2219	95	conclusive
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	92.8262	1695	2219	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	92.7664	1684	2219	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	85.0319	1430	2219	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	81.9202	1111	2219	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	81.1404	1042	2219	95	below_threshold
Mycolicibacterium neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	81.0894	1050	2219	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	80.76	989	2219	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	80.3838	918	2219	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.3411	918	2219	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.2876	671	2219	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.2729	966	2219	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.2375	865	2219	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.056	991	2219	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.0069	859	2219	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.9725	845	2219	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.7859	838	2219	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.3266	833	2219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:02,990] [INFO] DFAST Taxonomy check result was written to GCF_025822345.1_ASM2582234v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:02,990] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:02,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:02,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference/checkm_data
[2024-01-24 10:48:02,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:03,070] [INFO] Task started: CheckM
[2024-01-24 10:48:03,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822345.1_ASM2582234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822345.1_ASM2582234v1_genomic.fna/checkm_input GCF_025822345.1_ASM2582234v1_genomic.fna/checkm_result
[2024-01-24 10:49:16,378] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:16,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:16,412] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:16,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:16,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822345.1_ASM2582234v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:16,414] [INFO] Task started: Blastn
[2024-01-24 10:49:16,414] [INFO] Running command: blastn -query GCF_025822345.1_ASM2582234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2658bb9e-10b4-42f5-9046-9a6204216337/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822345.1_ASM2582234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:18,273] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:18,277] [INFO] Selected 21 target genomes.
[2024-01-24 10:49:18,277] [INFO] Target genome list was writen to GCF_025822345.1_ASM2582234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:18,314] [INFO] Task started: fastANI
[2024-01-24 10:49:18,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgba243f6e-397f-491f-830e-a5fdae00a935/GCF_025822345.1_ASM2582234v1_genomic.fna.gz --refList GCF_025822345.1_ASM2582234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822345.1_ASM2582234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:46,307] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:46,328] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:46,329] [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_002101555.1	s__Mycobacterium canariasense	99.9752	2169	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000613185.1	s__Mycobacterium cosmeticum	92.8371	1694	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_011758805.1	s__Mycobacterium fluoranthenivorans	85.0205	1432	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	-
GCA_016197365.1	s__Mycobacterium cosmeticum_A	84.734	1238	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	82.3197	1167	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_900078775.1	s__Mycobacterium aurum_A	82.1852	1086	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086115.1	s__Mycobacterium bacteremicum	81.9229	1111	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	81.8842	1072	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_001428895.1	s__Mycobacterium sp001428895	81.7596	1141	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	81.4388	1044	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	81.1231	1069	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_018326285.1	s__Mycobacterium sp018326285	80.9408	964	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000455325.1	s__Mycobacterium septicum	80.7586	985	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_001942045.1	s__Mycobacterium porcinum_A	80.6635	969	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001245615.1	s__Mycobacterium neworleansense	80.5975	988	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.5435	817	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295855.1	s__Mycobacterium fortuitum	80.4027	915	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_001665685.1	s__Mycobacterium sp001665685	80.3198	1004	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	80.1624	958	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_010726645.1	s__Mycobacterium duvalii	79.8883	853	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010729895.1	s__Mycobacterium confluentis	79.7165	849	2219	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:46,330] [INFO] GTDB search result was written to GCF_025822345.1_ASM2582234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:46,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:46,338] [INFO] DFAST_QC result json was written to GCF_025822345.1_ASM2582234v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:46,339] [INFO] DFAST_QC completed!
[2024-01-24 10:49:46,339] [INFO] Total running time: 0h2m37s