[2024-01-25 18:03:05,526] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:05,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:05,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference
[2024-01-25 18:03:06,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:06,658] [INFO] Task started: Prodigal
[2024-01-25 18:03:06,658] [INFO] Running command: gunzip -c /var/lib/cwl/stg60a80e77-6589-4a3a-9c1d-363b67b16897/GCF_025821825.1_ASM2582182v1_genomic.fna.gz | prodigal -d GCF_025821825.1_ASM2582182v1_genomic.fna/cds.fna -a GCF_025821825.1_ASM2582182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:23,611] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:23,611] [INFO] Task started: HMMsearch
[2024-01-25 18:03:23,611] [INFO] Running command: hmmsearch --tblout GCF_025821825.1_ASM2582182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference/reference_markers.hmm GCF_025821825.1_ASM2582182v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:23,867] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:23,868] [INFO] Found 6/6 markers.
[2024-01-25 18:03:23,916] [INFO] Query marker FASTA was written to GCF_025821825.1_ASM2582182v1_genomic.fna/markers.fasta
[2024-01-25 18:03:23,917] [INFO] Task started: Blastn
[2024-01-25 18:03:23,917] [INFO] Running command: blastn -query GCF_025821825.1_ASM2582182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference/reference_markers.fasta -out GCF_025821825.1_ASM2582182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:24,980] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:24,983] [INFO] Selected 13 target genomes.
[2024-01-25 18:03:24,983] [INFO] Target genome list was writen to GCF_025821825.1_ASM2582182v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:24,992] [INFO] Task started: fastANI
[2024-01-25 18:03:24,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg60a80e77-6589-4a3a-9c1d-363b67b16897/GCF_025821825.1_ASM2582182v1_genomic.fna.gz --refList GCF_025821825.1_ASM2582182v1_genomic.fna/target_genomes.txt --output GCF_025821825.1_ASM2582182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:43,645] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:43,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:43,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:43,660] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:03:43,660] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:43,660] [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 kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	99.9925	1882	1885	95	conclusive
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	99.9815	1868	1885	95	conclusive
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	99.9636	1841	1885	95	conclusive
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	81.5333	976	1885	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.4856	1094	1885	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	81.4453	1013	1885	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.267	1099	1885	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.0984	997	1885	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	81.087	1034	1885	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	80.9818	1148	1885	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	80.9712	1138	1885	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.5328	1003	1885	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	80.4751	1005	1885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:43,664] [INFO] DFAST Taxonomy check result was written to GCF_025821825.1_ASM2582182v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:43,665] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:43,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:43,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference/checkm_data
[2024-01-25 18:03:43,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:43,725] [INFO] Task started: CheckM
[2024-01-25 18:03:43,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821825.1_ASM2582182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821825.1_ASM2582182v1_genomic.fna/checkm_input GCF_025821825.1_ASM2582182v1_genomic.fna/checkm_result
[2024-01-25 18:04:33,917] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:33,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:33,938] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:33,939] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:33,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821825.1_ASM2582182v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:33,940] [INFO] Task started: Blastn
[2024-01-25 18:04:33,940] [INFO] Running command: blastn -query GCF_025821825.1_ASM2582182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39387cc5-190d-457b-91c8-3ca3ab5be8e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821825.1_ASM2582182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:35,509] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:35,512] [INFO] Selected 19 target genomes.
[2024-01-25 18:04:35,512] [INFO] Target genome list was writen to GCF_025821825.1_ASM2582182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:35,527] [INFO] Task started: fastANI
[2024-01-25 18:04:35,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg60a80e77-6589-4a3a-9c1d-363b67b16897/GCF_025821825.1_ASM2582182v1_genomic.fna.gz --refList GCF_025821825.1_ASM2582182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821825.1_ASM2582182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:00,156] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:00,168] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:00,168] [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_015689175.1	s__Mycobacterium kubicae	99.9925	1882	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	conclusive
GCF_001673155.1	s__Mycobacterium sp001673155	86.3128	1366	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	81.4722	1095	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001673535.1	s__Mycobacterium sp001673535	81.2828	1042	1885	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	81.2253	1024	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	81.2091	882	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900157385.1	s__Mycobacterium terramassiliense	81.156	1066	1885	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	81.1369	1031	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	81.1182	1067	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	81.1001	1032	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_002102155.1	s__Mycobacterium europaeum	81.0138	1023	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001672755.1	s__Mycobacterium colombiense_C	81.0013	976	1885	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	80.9912	1147	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_001673635.1	s__Mycobacterium asiaticum_C	80.9467	1102	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001417955.2	s__Mycobacterium gordonae_B	80.8526	1125	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613245.1	s__Mycobacterium asiaticum	80.6997	1130	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	-
GCF_002086675.1	s__Mycobacterium persicum	80.5377	1002	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_900232995.1	s__Mycobacterium simulans	80.5149	1000	1885	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_002104675.1	s__Mycobacterium decipiens	80.4007	917	1885	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 18:05:00,173] [INFO] GTDB search result was written to GCF_025821825.1_ASM2582182v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:00,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:00,177] [INFO] DFAST_QC result json was written to GCF_025821825.1_ASM2582182v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:00,177] [INFO] DFAST_QC completed!
[2024-01-25 18:05:00,177] [INFO] Total running time: 0h1m55s