[2024-01-24 13:21:46,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference
[2024-01-24 13:21:47,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,607] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cab02a9-e890-4ff7-af89-ef6663c7cd6a/GCF_002086755.1_ASM208675v1_genomic.fna.gz | prodigal -d GCF_002086755.1_ASM208675v1_genomic.fna/cds.fna -a GCF_002086755.1_ASM208675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:03,580] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:03,580] [INFO] Task started: HMMsearch
[2024-01-24 13:22:03,580] [INFO] Running command: hmmsearch --tblout GCF_002086755.1_ASM208675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference/reference_markers.hmm GCF_002086755.1_ASM208675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:03,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:03,840] [INFO] Found 6/6 markers.
[2024-01-24 13:22:03,891] [INFO] Query marker FASTA was written to GCF_002086755.1_ASM208675v1_genomic.fna/markers.fasta
[2024-01-24 13:22:03,892] [INFO] Task started: Blastn
[2024-01-24 13:22:03,892] [INFO] Running command: blastn -query GCF_002086755.1_ASM208675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference/reference_markers.fasta -out GCF_002086755.1_ASM208675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:04,942] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:04,945] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:04,946] [INFO] Target genome list was writen to GCF_002086755.1_ASM208675v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:04,952] [INFO] Task started: fastANI
[2024-01-24 13:22:04,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cab02a9-e890-4ff7-af89-ef6663c7cd6a/GCF_002086755.1_ASM208675v1_genomic.fna.gz --refList GCF_002086755.1_ASM208675v1_genomic.fna/target_genomes.txt --output GCF_002086755.1_ASM208675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:26,744] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:26,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:26,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:26,764] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:26,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:26,765] [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 shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	100.0	1394	1398	95	conclusive
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	99.9809	1397	1398	95	conclusive
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	83.5202	1080	1398	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	83.4375	1108	1398	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	83.4261	1051	1398	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	82.7411	910	1398	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	82.5865	1055	1398	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	82.3075	1059	1398	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	82.2832	1021	1398	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	82.2142	853	1398	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	82.1712	913	1398	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	82.1069	806	1398	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.976	1037	1398	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	81.7488	1030	1398	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.453	873	1398	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	81.3195	830	1398	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	81.2548	873	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:26,770] [INFO] DFAST Taxonomy check result was written to GCF_002086755.1_ASM208675v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:26,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:26,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:26,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference/checkm_data
[2024-01-24 13:22:26,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:26,818] [INFO] Task started: CheckM
[2024-01-24 13:22:26,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086755.1_ASM208675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086755.1_ASM208675v1_genomic.fna/checkm_input GCF_002086755.1_ASM208675v1_genomic.fna/checkm_result
[2024-01-24 13:23:12,687] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:12,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:12,709] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:12,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:12,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086755.1_ASM208675v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:12,710] [INFO] Task started: Blastn
[2024-01-24 13:23:12,710] [INFO] Running command: blastn -query GCF_002086755.1_ASM208675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5a050f-a99d-4b98-bc8d-91d6ab4768b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086755.1_ASM208675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:14,170] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:14,174] [INFO] Selected 19 target genomes.
[2024-01-24 13:23:14,174] [INFO] Target genome list was writen to GCF_002086755.1_ASM208675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:14,210] [INFO] Task started: fastANI
[2024-01-24 13:23:14,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cab02a9-e890-4ff7-af89-ef6663c7cd6a/GCF_002086755.1_ASM208675v1_genomic.fna.gz --refList GCF_002086755.1_ASM208675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086755.1_ASM208675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:38,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:38,037] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:38,038] [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_010730055.1	s__Mycobacterium shinjukuense	99.9809	1397	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000195955.2	s__Mycobacterium tuberculosis	83.4416	1050	1398	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	83.4144	1111	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	82.9055	900	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_010730745.1	s__Mycobacterium heidelbergense	82.7523	908	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002104675.1	s__Mycobacterium decipiens	82.6998	993	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101845.1	s__Mycobacterium riyadhense	82.5754	1060	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_900232995.1	s__Mycobacterium simulans	82.3209	1057	1398	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	82.2926	1019	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002101815.1	s__Mycobacterium paraense	82.1946	910	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667015.1	s__Mycobacterium sp001667015	82.1027	885	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	82.0287	879	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	81.9693	1037	1398	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	81.9065	900	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	81.8631	949	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116635.1	s__Mycobacterium szulgai	81.7224	1037	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	81.2949	834	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_000340435.2	s__Mycobacterium haemophilum	81.2626	872	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	-
GCF_008370645.1	s__Mycobacterium simiae_A	80.9	900	1398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:38,039] [INFO] GTDB search result was written to GCF_002086755.1_ASM208675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:38,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:38,043] [INFO] DFAST_QC result json was written to GCF_002086755.1_ASM208675v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:38,044] [INFO] DFAST_QC completed!
[2024-01-24 13:23:38,044] [INFO] Total running time: 0h1m52s