[2024-01-25 19:12:20,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:20,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:20,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference
[2024-01-25 19:12:21,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:21,858] [INFO] Task started: Prodigal
[2024-01-25 19:12:21,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa4d5705-6132-4201-a346-95b9fba1e9ed/GCF_025822405.1_ASM2582240v1_genomic.fna.gz | prodigal -d GCF_025822405.1_ASM2582240v1_genomic.fna/cds.fna -a GCF_025822405.1_ASM2582240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:44,705] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:44,705] [INFO] Task started: HMMsearch
[2024-01-25 19:12:44,705] [INFO] Running command: hmmsearch --tblout GCF_025822405.1_ASM2582240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference/reference_markers.hmm GCF_025822405.1_ASM2582240v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:45,023] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:45,024] [INFO] Found 6/6 markers.
[2024-01-25 19:12:45,074] [INFO] Query marker FASTA was written to GCF_025822405.1_ASM2582240v1_genomic.fna/markers.fasta
[2024-01-25 19:12:45,075] [INFO] Task started: Blastn
[2024-01-25 19:12:45,075] [INFO] Running command: blastn -query GCF_025822405.1_ASM2582240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference/reference_markers.fasta -out GCF_025822405.1_ASM2582240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:46,138] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:46,140] [INFO] Selected 18 target genomes.
[2024-01-25 19:12:46,140] [INFO] Target genome list was writen to GCF_025822405.1_ASM2582240v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:46,169] [INFO] Task started: fastANI
[2024-01-25 19:12:46,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa4d5705-6132-4201-a346-95b9fba1e9ed/GCF_025822405.1_ASM2582240v1_genomic.fna.gz --refList GCF_025822405.1_ASM2582240v1_genomic.fna/target_genomes.txt --output GCF_025822405.1_ASM2582240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:15,704] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:15,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:15,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:15,720] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:13:15,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:13:15,720] [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 angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	99.9195	2051	2196	95	conclusive
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	93.1588	1884	2196	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	81.9709	1090	2196	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	81.9642	1057	2196	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	81.9361	1098	2196	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	81.8997	1089	2196	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	81.3622	1203	2196	95	below_threshold
Mycobacterium gastri	strain=DSM 43505	GCA_002102175.1	1777	1777	type	True	81.3622	1210	2196	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	81.281	1123	2196	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	81.2368	1260	2196	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	81.1998	1104	2196	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	81.178	1110	2196	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.112	1066	2196	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	80.9083	1223	2196	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	80.8661	1067	2196	95	below_threshold
Mycobacterium attenuatum	strain=MK41	GCA_900566085.1	2341086	2341086	type	True	80.8315	1210	2196	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	80.8288	1065	2196	95	below_threshold
Mycobacterium basiliense		GCA_900292015.1	2094119	2094119	type	True	80.009	1108	2196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:15,721] [INFO] DFAST Taxonomy check result was written to GCF_025822405.1_ASM2582240v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:15,722] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:15,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:15,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference/checkm_data
[2024-01-25 19:13:15,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:15,786] [INFO] Task started: CheckM
[2024-01-25 19:13:15,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822405.1_ASM2582240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822405.1_ASM2582240v1_genomic.fna/checkm_input GCF_025822405.1_ASM2582240v1_genomic.fna/checkm_result
[2024-01-25 19:14:28,882] [INFO] Task succeeded: CheckM
[2024-01-25 19:14:28,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:14:28,944] [INFO] ===== Completeness check finished =====
[2024-01-25 19:14:28,944] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:14:28,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822405.1_ASM2582240v1_genomic.fna/markers.fasta)
[2024-01-25 19:14:28,946] [INFO] Task started: Blastn
[2024-01-25 19:14:28,946] [INFO] Running command: blastn -query GCF_025822405.1_ASM2582240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd6cb0f5-1e49-418d-955a-8230cdf2a768/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822405.1_ASM2582240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:14:30,582] [INFO] Task succeeded: Blastn
[2024-01-25 19:14:30,585] [INFO] Selected 19 target genomes.
[2024-01-25 19:14:30,586] [INFO] Target genome list was writen to GCF_025822405.1_ASM2582240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:14:30,620] [INFO] Task started: fastANI
[2024-01-25 19:14:30,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa4d5705-6132-4201-a346-95b9fba1e9ed/GCF_025822405.1_ASM2582240v1_genomic.fna.gz --refList GCF_025822405.1_ASM2582240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822405.1_ASM2582240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:15:02,225] [INFO] Task succeeded: fastANI
[2024-01-25 19:15:02,237] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:15:02,237] [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_002086155.1	s__Mycobacterium angelicum	99.9195	2051	2196	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_002116635.1	s__Mycobacterium szulgai	93.1403	1886	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730745.1	s__Mycobacterium heidelbergense	81.9244	1100	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010730055.1	s__Mycobacterium shinjukuense	81.9182	1089	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001954275.1	s__Mycobacterium sp001954275	81.3912	1074	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_900566055.1	s__Mycobacterium innocens	81.3662	1202	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_015689175.1	s__Mycobacterium kubicae	81.2621	1127	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_003614435.1	s__Mycobacterium paragordonae	81.2429	1267	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.2259	1260	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_000277125.1	s__Mycobacterium intracellulare	81.1721	1089	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_002104675.1	s__Mycobacterium decipiens	81.1094	1121	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667115.1	s__Mycobacterium sp001667115	80.957	1103	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673155.1	s__Mycobacterium sp001673155	80.9171	996	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101675.1	s__Mycobacterium gordonae	80.8808	1227	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_010731675.1	s__Mycobacterium marseillense	80.8481	1070	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCA_019247635.1	s__Mycobacterium sp019247635	80.8471	975	2196	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	80.8214	1213	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.59	99.54	0.94	0.93	4	-
GCF_001673315.1	s__Mycobacterium asiaticum_B	80.6154	1035	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292015.1	s__Mycobacterium basiliense	80.0395	1099	2196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:15:02,242] [INFO] GTDB search result was written to GCF_025822405.1_ASM2582240v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:15:02,242] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:15:02,247] [INFO] DFAST_QC result json was written to GCF_025822405.1_ASM2582240v1_genomic.fna/dqc_result.json
[2024-01-25 19:15:02,247] [INFO] DFAST_QC completed!
[2024-01-25 19:15:02,247] [INFO] Total running time: 0h2m42s