[2024-01-24 13:56:57,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:57,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:57,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference
[2024-01-24 13:56:58,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:58,324] [INFO] Task started: Prodigal
[2024-01-24 13:56:58,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg381a3c19-916f-4a49-ace6-445725212644/GCF_001969965.1_Sparso1.0_genomic.fna.gz | prodigal -d GCF_001969965.1_Sparso1.0_genomic.fna/cds.fna -a GCF_001969965.1_Sparso1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:26,590] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:26,591] [INFO] Task started: HMMsearch
[2024-01-24 13:57:26,591] [INFO] Running command: hmmsearch --tblout GCF_001969965.1_Sparso1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference/reference_markers.hmm GCF_001969965.1_Sparso1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:27,111] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:27,113] [INFO] Found 6/6 markers.
[2024-01-24 13:57:27,189] [INFO] Query marker FASTA was written to GCF_001969965.1_Sparso1.0_genomic.fna/markers.fasta
[2024-01-24 13:57:27,190] [INFO] Task started: Blastn
[2024-01-24 13:57:27,190] [INFO] Running command: blastn -query GCF_001969965.1_Sparso1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference/reference_markers.fasta -out GCF_001969965.1_Sparso1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:28,557] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:28,561] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:28,562] [INFO] Target genome list was writen to GCF_001969965.1_Sparso1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:57:28,572] [INFO] Task started: fastANI
[2024-01-24 13:57:28,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg381a3c19-916f-4a49-ace6-445725212644/GCF_001969965.1_Sparso1.0_genomic.fna.gz --refList GCF_001969965.1_Sparso1.0_genomic.fna/target_genomes.txt --output GCF_001969965.1_Sparso1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:10,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:10,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:10,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:10,485] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:10,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:10,486] [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 sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	100.0	2886	2912	95	conclusive
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	99.7959	2507	2912	95	conclusive
Streptomyces milbemycinicus	strain=NRRL 5739	GCA_002154605.1	476552	476552	type	True	89.311	1844	2912	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	85.0603	1646	2912	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	84.6364	1867	2912	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	84.6264	1856	2912	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	84.5869	1775	2912	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	84.5715	1568	2912	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	84.5461	1491	2912	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	82.7104	1224	2912	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.5554	1286	2912	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	81.113	1133	2912	95	below_threshold
Streptomyces thermoviolaceus subsp. apingens	strain=JCM 4312	GCA_014649255.1	66859	1952	type	True	80.9371	1067	2912	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	80.9208	1108	2912	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	80.8308	1056	2912	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	80.8149	1071	2912	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.719	1349	2912	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.622	1320	2912	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	80.5608	1291	2912	95	below_threshold
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	76.4356	686	2912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:10,488] [INFO] DFAST Taxonomy check result was written to GCF_001969965.1_Sparso1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:58:10,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:10,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:10,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference/checkm_data
[2024-01-24 13:58:10,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:10,587] [INFO] Task started: CheckM
[2024-01-24 13:58:10,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001969965.1_Sparso1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001969965.1_Sparso1.0_genomic.fna/checkm_input GCF_001969965.1_Sparso1.0_genomic.fna/checkm_result
[2024-01-24 13:59:58,986] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:58,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:59,013] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:59,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:59,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001969965.1_Sparso1.0_genomic.fna/markers.fasta)
[2024-01-24 13:59:59,014] [INFO] Task started: Blastn
[2024-01-24 13:59:59,015] [INFO] Running command: blastn -query GCF_001969965.1_Sparso1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d333ad8-16d9-4834-ba46-2030bfb41556/dqc_reference/reference_markers_gtdb.fasta -out GCF_001969965.1_Sparso1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:01,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:01,287] [INFO] Selected 15 target genomes.
[2024-01-24 14:00:01,288] [INFO] Target genome list was writen to GCF_001969965.1_Sparso1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:01,308] [INFO] Task started: fastANI
[2024-01-24 14:00:01,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg381a3c19-916f-4a49-ace6-445725212644/GCF_001969965.1_Sparso1.0_genomic.fna.gz --refList GCF_001969965.1_Sparso1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_001969965.1_Sparso1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:38,469] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:38,483] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:38,483] [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_001704635.1	s__Streptomyces sparsogenes	99.8089	2506	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	conclusive
GCF_002224125.1	s__Streptomyces sp002224125	89.9054	2191	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154605.1	s__Streptomyces milbemycinicus	89.301	1845	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001553455.1	s__Streptomyces hygroscopicus	85.043	1648	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_001417735.1	s__Streptomyces sp001417735	85.0236	1707	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005405945.1	s__Streptomyces violaceusniger	84.6919	1857	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_018138715.1	s__Streptomyces asiaticus	84.5254	1864	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_013364155.1	s__Streptomyces sp013364155	84.3206	1627	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	84.3143	1789	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_000158915.1	s__Streptomyces himastatinicus	84.2766	1773	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	-
GCF_016741875.1	s__Streptomyces coffeae	84.1367	1617	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	82.7993	1388	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	80.9352	1282	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	80.7483	1197	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_008704425.1	s__Streptomyces fradiae	80.5442	1168	2912	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:38,485] [INFO] GTDB search result was written to GCF_001969965.1_Sparso1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:38,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:38,491] [INFO] DFAST_QC result json was written to GCF_001969965.1_Sparso1.0_genomic.fna/dqc_result.json
[2024-01-24 14:00:38,492] [INFO] DFAST_QC completed!
[2024-01-24 14:00:38,492] [INFO] Total running time: 0h3m41s