[2024-01-24 11:34:52,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:52,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:52,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference
[2024-01-24 11:34:55,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,643] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,643] [INFO] Running command: gunzip -c /var/lib/cwl/stge57c25dd-5c1d-4a7f-8417-372c3450c46b/GCF_001896135.2_ASM189613v2_genomic.fna.gz | prodigal -d GCF_001896135.2_ASM189613v2_genomic.fna/cds.fna -a GCF_001896135.2_ASM189613v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:19,459] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:19,460] [INFO] Task started: HMMsearch
[2024-01-24 11:35:19,460] [INFO] Running command: hmmsearch --tblout GCF_001896135.2_ASM189613v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference/reference_markers.hmm GCF_001896135.2_ASM189613v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:19,842] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:19,844] [INFO] Found 6/6 markers.
[2024-01-24 11:35:19,913] [INFO] Query marker FASTA was written to GCF_001896135.2_ASM189613v2_genomic.fna/markers.fasta
[2024-01-24 11:35:19,913] [INFO] Task started: Blastn
[2024-01-24 11:35:19,913] [INFO] Running command: blastn -query GCF_001896135.2_ASM189613v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference/reference_markers.fasta -out GCF_001896135.2_ASM189613v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:21,235] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:21,238] [INFO] Selected 31 target genomes.
[2024-01-24 11:35:21,239] [INFO] Target genome list was writen to GCF_001896135.2_ASM189613v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:21,250] [INFO] Task started: fastANI
[2024-01-24 11:35:21,251] [INFO] Running command: fastANI --query /var/lib/cwl/stge57c25dd-5c1d-4a7f-8417-372c3450c46b/GCF_001896135.2_ASM189613v2_genomic.fna.gz --refList GCF_001896135.2_ASM189613v2_genomic.fna/target_genomes.txt --output GCF_001896135.2_ASM189613v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:24,610] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:24,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:24,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:24,636] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:24,636] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:24,637] [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
Streptomyces galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	93.7125	2122	2841	95	below_threshold
Streptomyces galilaeus	strain=JCM 4757	GCA_014650835.1	33899	33899	type	True	93.2645	2248	2841	95	below_threshold
Streptomyces bobili	strain=NRRL B-1338	GCA_002154575.1	67280	67280	type	True	93.2	1775	2841	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	86.8368	2062	2841	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	86.3932	1976	2841	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	86.3869	1929	2841	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	86.3465	1979	2841	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	86.3241	1885	2841	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.3205	1578	2841	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	86.0399	1827	2841	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.1717	1886	2841	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.0619	1846	2841	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	85.0421	1855	2841	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.0253	1793	2841	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	84.9792	1943	2841	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	84.8975	1900	2841	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	84.8593	1934	2841	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.7992	1683	2841	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.6964	1659	2841	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.5922	1714	2841	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	84.5484	1840	2841	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.9947	1540	2841	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	81.7109	821	2841	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	81.6544	1320	2841	95	below_threshold
Streptomyces laurentii	strain=ATCC 31255	GCA_002355495.1	39478	39478	type	True	81.3047	1358	2841	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	81.259	1271	2841	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	81.2273	1259	2841	95	below_threshold
Streptomyces toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	81.1637	1276	2841	95	below_threshold
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	80.4993	913	2841	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.0561	824	2841	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	79.4519	1089	2841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:24,638] [INFO] DFAST Taxonomy check result was written to GCF_001896135.2_ASM189613v2_genomic.fna/tc_result.tsv
[2024-01-24 11:36:24,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:24,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:24,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference/checkm_data
[2024-01-24 11:36:24,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:24,736] [INFO] Task started: CheckM
[2024-01-24 11:36:24,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001896135.2_ASM189613v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001896135.2_ASM189613v2_genomic.fna/checkm_input GCF_001896135.2_ASM189613v2_genomic.fna/checkm_result
[2024-01-24 11:38:14,800] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:14,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 11:38:14,829] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:14,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:14,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001896135.2_ASM189613v2_genomic.fna/markers.fasta)
[2024-01-24 11:38:14,830] [INFO] Task started: Blastn
[2024-01-24 11:38:14,831] [INFO] Running command: blastn -query GCF_001896135.2_ASM189613v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgef6c7579-0900-4413-a331-b876f4de2c50/dqc_reference/reference_markers_gtdb.fasta -out GCF_001896135.2_ASM189613v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:16,884] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:16,889] [INFO] Selected 26 target genomes.
[2024-01-24 11:38:16,889] [INFO] Target genome list was writen to GCF_001896135.2_ASM189613v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:16,908] [INFO] Task started: fastANI
[2024-01-24 11:38:16,909] [INFO] Running command: fastANI --query /var/lib/cwl/stge57c25dd-5c1d-4a7f-8417-372c3450c46b/GCF_001896135.2_ASM189613v2_genomic.fna.gz --refList GCF_001896135.2_ASM189613v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001896135.2_ASM189613v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:39:11,652] [INFO] Task succeeded: fastANI
[2024-01-24 11:39:11,676] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:39:11,676] [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_001896135.2	s__Streptomyces phaeoluteigriseus	100.0	2838	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002154575.1	s__Streptomyces bobili	93.2076	1774	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.61	97.61	0.88	0.85	3	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	88.2417	2052	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217285.1	s__Streptomyces sp004217285	87.1451	1606	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	86.5248	1867	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_001514205.1	s__Streptomyces griseoruber	86.4271	1922	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112535.1	s__Streptomyces rishiriensis	86.3104	1888	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746365.1	s__Streptomyces sp001746365	86.2222	1886	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649655.1	s__Streptomyces humidus	86.049	1825	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514285.1	s__Streptomyces sp001514285	85.9753	1854	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003032475.1	s__Streptomyces sp003032475	85.858	1842	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	85.4666	1862	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721105.1	s__Streptomyces cellulosae_A	85.3572	1818	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	85.3342	1805	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720805.1	s__Streptomyces violaceoruber_B	85.2795	1811	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	85.2237	1643	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704715.1	s__Streptomyces chartreusis	84.9713	1944	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	-
GCF_019049285.1	s__Streptomyces sp019049285	84.9099	1834	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746295.1	s__Streptomyces sp001746295	84.8373	1886	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675325.1	s__Streptomyces sp003675325	84.4402	1682	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	84.1814	1742	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.2597	1479	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_008704425.1	s__Streptomyces fradiae	81.2407	1275	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_003323715.1	s__Streptomyces diacarni	79.4634	1087	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720635.1	s__Kitasatospora sp000720635	78.6003	1063	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	78.5211	1001	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:39:11,678] [INFO] GTDB search result was written to GCF_001896135.2_ASM189613v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:39:11,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:39:11,684] [INFO] DFAST_QC result json was written to GCF_001896135.2_ASM189613v2_genomic.fna/dqc_result.json
[2024-01-24 11:39:11,684] [INFO] DFAST_QC completed!
[2024-01-24 11:39:11,685] [INFO] Total running time: 0h4m19s