[2023-03-15 07:25:31,268] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference
[2023-03-15 07:25:32,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,917] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,917] [INFO] Running command: cat /var/lib/cwl/stg3ff25e86-06ea-4dc6-a549-16ca518ccc4d/OceanDNA-b2838.fa | prodigal -d OceanDNA-b2838/cds.fna -a OceanDNA-b2838/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:53,090] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:53,090] [INFO] Task started: HMMsearch
[2023-03-15 07:25:53,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b2838/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference/reference_markers.hmm OceanDNA-b2838/protein.faa > /dev/null
[2023-03-15 07:25:53,287] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:53,288] [INFO] Found 6/6 markers.
[2023-03-15 07:25:53,336] [INFO] Query marker FASTA was written to OceanDNA-b2838/markers.fasta
[2023-03-15 07:25:53,336] [INFO] Task started: Blastn
[2023-03-15 07:25:53,336] [INFO] Running command: blastn -query OceanDNA-b2838/markers.fasta -db /var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference/reference_markers.fasta -out OceanDNA-b2838/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:54,325] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:54,331] [INFO] Selected 20 target genomes.
[2023-03-15 07:25:54,331] [INFO] Target genome list was writen to OceanDNA-b2838/target_genomes.txt
[2023-03-15 07:25:54,341] [INFO] Task started: fastANI
[2023-03-15 07:25:54,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff25e86-06ea-4dc6-a549-16ca518ccc4d/OceanDNA-b2838.fa --refList OceanDNA-b2838/target_genomes.txt --output OceanDNA-b2838/fastani_result.tsv --threads 1
[2023-03-15 07:26:11,772] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:11,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:26:11,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:26:11,784] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:26:11,784] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:26:11,785] [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 senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	81.2303	753	1068	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	81.2034	755	1068	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	81.1987	732	1068	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	81.1496	750	1068	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	81.0791	721	1068	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	80.9322	747	1068	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	80.8983	755	1068	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	80.6191	690	1068	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	80.4675	696	1068	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	80.4147	693	1068	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	80.3712	680	1068	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	79.8854	663	1068	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	79.7624	639	1068	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	79.637	514	1068	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.5382	595	1068	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.1723	589	1068	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.0818	595	1068	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	79.0352	561	1068	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	78.916	557	1068	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	78.8797	573	1068	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:26:11,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2838/tc_result.tsv
[2023-03-15 07:26:11,799] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:26:11,799] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:26:11,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference/checkm_data
[2023-03-15 07:26:11,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:26:11,871] [INFO] Task started: CheckM
[2023-03-15 07:26:11,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2838/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2838/checkm_input OceanDNA-b2838/checkm_result
[2023-03-15 07:27:04,726] [INFO] Task succeeded: CheckM
[2023-03-15 07:27:04,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:27:04,796] [INFO] ===== Completeness check finished =====
[2023-03-15 07:27:04,796] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:27:04,796] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2838/markers.fasta)
[2023-03-15 07:27:04,797] [INFO] Task started: Blastn
[2023-03-15 07:27:04,797] [INFO] Running command: blastn -query OceanDNA-b2838/markers.fasta -db /var/lib/cwl/stgaa69bd31-4fa9-41bc-a562-2f8940301e30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2838/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:27:06,234] [INFO] Task succeeded: Blastn
[2023-03-15 07:27:06,241] [INFO] Selected 19 target genomes.
[2023-03-15 07:27:06,241] [INFO] Target genome list was writen to OceanDNA-b2838/target_genomes_gtdb.txt
[2023-03-15 07:27:06,258] [INFO] Task started: fastANI
[2023-03-15 07:27:06,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff25e86-06ea-4dc6-a549-16ca518ccc4d/OceanDNA-b2838.fa --refList OceanDNA-b2838/target_genomes_gtdb.txt --output OceanDNA-b2838/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:27:24,471] [INFO] Task succeeded: fastANI
[2023-03-15 07:27:24,482] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:27:24,482] [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_001667375.1	s__Mycobacterium sinense_A	81.298	748	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_002102265.1	s__Mycobacterium longobardum	81.1867	735	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667945.1	s__Mycobacterium sinense_B	81.1664	751	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCA_004354905.1	s__Mycobacterium eburneum	81.1364	742	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_002086455.1	s__Mycobacterium algericum	81.0162	775	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_003284925.1	s__Mycobacterium algericum_A	80.9658	687	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727125.1	s__Mycobacterium terrae	80.8568	759	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001668625.1	s__Mycobacterium sp001668625	80.7893	699	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101585.1	s__Mycobacterium engbaekii	80.593	693	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_001673105.1	s__Mycobacterium heraklionense_A	80.5174	693	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	80.4816	693	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_010729485.1	s__Mycobacterium hiberniae	80.3957	696	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
GCF_010731755.1	s__Mycobacterium minnesotense	79.8846	661	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101595.1	s__Mycobacterium celatum	79.7585	640	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007714205.1	s__Mycobacterium helveticum	79.5122	598	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002102155.1	s__Mycobacterium europaeum	79.3893	629	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001953985.1	s__Mycobacterium colombiense_B	79.2811	613	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_002104765.1	s__Mycobacterium vulneris	79.1917	587	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	79.1832	623	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-15 07:27:24,486] [INFO] GTDB search result was written to OceanDNA-b2838/result_gtdb.tsv
[2023-03-15 07:27:24,490] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:27:24,497] [INFO] DFAST_QC result json was written to OceanDNA-b2838/dqc_result.json
[2023-03-15 07:27:24,497] [INFO] DFAST_QC completed!
[2023-03-15 07:27:24,498] [INFO] Total running time: 0h1m53s