[2024-01-25 17:58:50,637] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference
[2024-01-25 17:58:51,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,780] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,780] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8d177ba-16a4-44c9-89a4-02a7970bd946/GCF_022370835.2_ASM2237083v2_genomic.fna.gz | prodigal -d GCF_022370835.2_ASM2237083v2_genomic.fna/cds.fna -a GCF_022370835.2_ASM2237083v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:02,525] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:02,525] [INFO] Task started: HMMsearch
[2024-01-25 17:59:02,525] [INFO] Running command: hmmsearch --tblout GCF_022370835.2_ASM2237083v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference/reference_markers.hmm GCF_022370835.2_ASM2237083v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:02,725] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:02,726] [INFO] Found 6/6 markers.
[2024-01-25 17:59:02,757] [INFO] Query marker FASTA was written to GCF_022370835.2_ASM2237083v2_genomic.fna/markers.fasta
[2024-01-25 17:59:02,757] [INFO] Task started: Blastn
[2024-01-25 17:59:02,757] [INFO] Running command: blastn -query GCF_022370835.2_ASM2237083v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference/reference_markers.fasta -out GCF_022370835.2_ASM2237083v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:03,922] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:03,924] [INFO] Selected 23 target genomes.
[2024-01-25 17:59:03,925] [INFO] Target genome list was writen to GCF_022370835.2_ASM2237083v2_genomic.fna/target_genomes.txt
[2024-01-25 17:59:03,942] [INFO] Task started: fastANI
[2024-01-25 17:59:03,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8d177ba-16a4-44c9-89a4-02a7970bd946/GCF_022370835.2_ASM2237083v2_genomic.fna.gz --refList GCF_022370835.2_ASM2237083v2_genomic.fna/target_genomes.txt --output GCF_022370835.2_ASM2237083v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:25,506] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:25,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:25,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:25,520] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:25,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:25,521] [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
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	80.9062	828	1311	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	80.6874	829	1311	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	80.6791	788	1311	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	80.6646	857	1311	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	80.6467	798	1311	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	80.6281	811	1311	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	80.4891	796	1311	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.4702	733	1311	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.3962	750	1311	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.3694	731	1311	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.3587	763	1311	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.3582	752	1311	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	80.1157	758	1311	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.1124	719	1311	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	80.0011	715	1311	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	79.9626	680	1311	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	79.9388	734	1311	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	79.8944	678	1311	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	79.8928	729	1311	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	79.6414	731	1311	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	79.641	716	1311	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	78.7965	609	1311	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	78.7681	604	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:25,525] [INFO] DFAST Taxonomy check result was written to GCF_022370835.2_ASM2237083v2_genomic.fna/tc_result.tsv
[2024-01-25 17:59:25,525] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:25,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:25,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference/checkm_data
[2024-01-25 17:59:25,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:25,574] [INFO] Task started: CheckM
[2024-01-25 17:59:25,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022370835.2_ASM2237083v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022370835.2_ASM2237083v2_genomic.fna/checkm_input GCF_022370835.2_ASM2237083v2_genomic.fna/checkm_result
[2024-01-25 18:00:22,102] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:22,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:22,133] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:22,133] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:22,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022370835.2_ASM2237083v2_genomic.fna/markers.fasta)
[2024-01-25 18:00:22,134] [INFO] Task started: Blastn
[2024-01-25 18:00:22,135] [INFO] Running command: blastn -query GCF_022370835.2_ASM2237083v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ff1a66-9758-4b31-9c36-d2ad9f5eb86c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022370835.2_ASM2237083v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:23,806] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:23,809] [INFO] Selected 19 target genomes.
[2024-01-25 18:00:23,809] [INFO] Target genome list was writen to GCF_022370835.2_ASM2237083v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:23,828] [INFO] Task started: fastANI
[2024-01-25 18:00:23,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8d177ba-16a4-44c9-89a4-02a7970bd946/GCF_022370835.2_ASM2237083v2_genomic.fna.gz --refList GCF_022370835.2_ASM2237083v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022370835.2_ASM2237083v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:00:43,490] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:43,501] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:00:43,502] [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_002104795.1	s__Mycobacterium koreense	89.51	1034	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	98.84	0.96	0.92	3	-
GCF_001668625.1	s__Mycobacterium sp001668625	84.3413	893	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102395.1	s__Mycobacterium triviale	83.8277	925	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354905.1	s__Mycobacterium eburneum	81.6432	864	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_018455725.1	s__Mycobacterium sp018455725	81.208	758	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086285.1	s__Mycobacterium kumamotonense	80.9348	824	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_001667375.1	s__Mycobacterium sinense_A	80.8648	784	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_002086455.1	s__Mycobacterium algericum	80.7582	803	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_001667945.1	s__Mycobacterium sinense_B	80.722	799	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_002101885.1	s__Mycobacterium senuense	80.7037	826	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010727125.1	s__Mycobacterium terrae	80.623	810	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_010726955.1	s__Mycobacterium fallax	80.5011	728	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_002102265.1	s__Mycobacterium longobardum	80.4934	795	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.1941	687	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	80.0629	722	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000613185.1	s__Mycobacterium cosmeticum	79.8914	679	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002105755.1	s__Mycobacterium colombiense	79.6538	728	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001672755.1	s__Mycobacterium colombiense_C	79.3041	694	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245755.1	s__Mycobacterium sp019245755	78.9169	585	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.79	99.79	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:00:43,503] [INFO] GTDB search result was written to GCF_022370835.2_ASM2237083v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:00:43,503] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:00:43,507] [INFO] DFAST_QC result json was written to GCF_022370835.2_ASM2237083v2_genomic.fna/dqc_result.json
[2024-01-25 18:00:43,507] [INFO] DFAST_QC completed!
[2024-01-25 18:00:43,507] [INFO] Total running time: 0h1m53s