[2024-01-25 19:11:20,736] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:20,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:20,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference
[2024-01-25 19:11:21,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:21,906] [INFO] Task started: Prodigal
[2024-01-25 19:11:21,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg704d7454-38c3-4367-99d7-d43d90401d2f/GCF_025165795.1_ASM2516579v1_genomic.fna.gz | prodigal -d GCF_025165795.1_ASM2516579v1_genomic.fna/cds.fna -a GCF_025165795.1_ASM2516579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:41,121] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:41,121] [INFO] Task started: HMMsearch
[2024-01-25 19:11:41,121] [INFO] Running command: hmmsearch --tblout GCF_025165795.1_ASM2516579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference/reference_markers.hmm GCF_025165795.1_ASM2516579v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:41,444] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:41,445] [INFO] Found 6/6 markers.
[2024-01-25 19:11:41,503] [INFO] Query marker FASTA was written to GCF_025165795.1_ASM2516579v1_genomic.fna/markers.fasta
[2024-01-25 19:11:41,504] [INFO] Task started: Blastn
[2024-01-25 19:11:41,504] [INFO] Running command: blastn -query GCF_025165795.1_ASM2516579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference/reference_markers.fasta -out GCF_025165795.1_ASM2516579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:42,703] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:42,705] [INFO] Selected 28 target genomes.
[2024-01-25 19:11:42,706] [INFO] Target genome list was writen to GCF_025165795.1_ASM2516579v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:42,727] [INFO] Task started: fastANI
[2024-01-25 19:11:42,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg704d7454-38c3-4367-99d7-d43d90401d2f/GCF_025165795.1_ASM2516579v1_genomic.fna.gz --refList GCF_025165795.1_ASM2516579v1_genomic.fna/target_genomes.txt --output GCF_025165795.1_ASM2516579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:28,025] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:28,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:28,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:28,042] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:12:28,042] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:12:28,042] [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 armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	82.8953	1448	2484	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	80.7048	1053	2484	95	below_threshold
Streptomyces albidus (ex Kaewkla and Franco 2021)	strain=CAP215	GCA_013870515.1	722709	722709	type	True	80.6521	914	2484	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	80.6426	1163	2484	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.4356	1072	2484	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.3964	931	2484	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.302	791	2484	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.275	925	2484	95	below_threshold
Streptomyces purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	80.2493	997	2484	95	below_threshold
Streptomyces violens	strain=NRRL ISP-5597	GCA_000717745.1	66377	66377	type	True	80.098	1067	2484	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	80.0413	1071	2484	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.0229	1146	2484	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	80.0034	972	2484	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	79.9857	1138	2484	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	79.9697	1075	2484	95	below_threshold
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	79.9678	1053	2484	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.9511	1220	2484	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	79.94	975	2484	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	79.9073	1088	2484	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	79.8824	1050	2484	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.8475	1109	2484	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	79.833	931	2484	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	79.7699	908	2484	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	79.6244	1084	2484	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	79.5711	996	2484	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	79.3288	1025	2484	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.2961	1033	2484	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	79.1251	921	2484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:28,044] [INFO] DFAST Taxonomy check result was written to GCF_025165795.1_ASM2516579v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:28,044] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:28,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:28,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference/checkm_data
[2024-01-25 19:12:28,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:28,116] [INFO] Task started: CheckM
[2024-01-25 19:12:28,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025165795.1_ASM2516579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025165795.1_ASM2516579v1_genomic.fna/checkm_input GCF_025165795.1_ASM2516579v1_genomic.fna/checkm_result
[2024-01-25 19:14:06,133] [INFO] Task succeeded: CheckM
[2024-01-25 19:14:06,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:14:06,157] [INFO] ===== Completeness check finished =====
[2024-01-25 19:14:06,158] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:14:06,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025165795.1_ASM2516579v1_genomic.fna/markers.fasta)
[2024-01-25 19:14:06,159] [INFO] Task started: Blastn
[2024-01-25 19:14:06,159] [INFO] Running command: blastn -query GCF_025165795.1_ASM2516579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9db48b-72ed-4aa8-9fcf-76cb0745bbda/dqc_reference/reference_markers_gtdb.fasta -out GCF_025165795.1_ASM2516579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:14:08,154] [INFO] Task succeeded: Blastn
[2024-01-25 19:14:08,157] [INFO] Selected 23 target genomes.
[2024-01-25 19:14:08,157] [INFO] Target genome list was writen to GCF_025165795.1_ASM2516579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:14:08,211] [INFO] Task started: fastANI
[2024-01-25 19:14:08,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg704d7454-38c3-4367-99d7-d43d90401d2f/GCF_025165795.1_ASM2516579v1_genomic.fna.gz --refList GCF_025165795.1_ASM2516579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025165795.1_ASM2516579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:45,290] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:45,305] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:14:45,306] [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_000424825.1	s__Streptomyces sp000424825	86.1689	1583	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355155.1	s__Streptomyces armeniacus	82.8765	1451	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665095.1	s__Streptomyces sp003665095	82.037	1299	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426325.1	s__Streptomyces sp000426325	81.2392	1093	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.50	96.50	0.91	0.91	2	-
GCF_012726235.1	s__Streptomyces sp012726235	80.8867	1086	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676345.1	s__Streptomyces smyrnaeus	80.6515	1161	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_013870515.1	s__Streptomyces albidus	80.634	917	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424965.1	s__Streptomyces sp000424965	80.5993	1055	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204855.1	s__Streptomyces haliclonae	80.5168	1046	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676365.1	s__Streptomyces oryzae	80.4288	1073	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001751365.1	s__Streptomyces abyssalis	80.3053	1030	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.91	99.91	0.99	0.99	2	-
GCF_004684805.1	s__Streptomyces palmae	80.282	923	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424845.1	s__Streptomyces sp000424845	80.1834	885	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704655.1	s__Streptomyces rimosus	80.0639	1075	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
GCF_000715845.1	s__Streptomyces monomycini	79.9211	1085	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	79.7257	950	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	79.5503	1104	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556545.1	s__Streptomyces formicae	79.5499	1087	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000514715.1	s__Streptomyces sp000514715	79.441	1105	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514035.1	s__Streptomyces yokosukanensis	79.2929	1036	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	79.2786	1037	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_002847285.1	s__Streptomyces sp002847285	79.2761	1085	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
GCF_009604385.1	s__Streptomyces sp009604385	79.1061	925	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:45,310] [INFO] GTDB search result was written to GCF_025165795.1_ASM2516579v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:45,312] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:45,316] [INFO] DFAST_QC result json was written to GCF_025165795.1_ASM2516579v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:45,316] [INFO] DFAST_QC completed!
[2024-01-25 19:14:45,317] [INFO] Total running time: 0h3m25s