[2024-01-25 20:02:20,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:20,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:20,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference
[2024-01-25 20:02:21,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:21,676] [INFO] Task started: Prodigal
[2024-01-25 20:02:21,677] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd243361-347b-454a-938a-70749a87c028/GCF_007097205.2_ASM709720v2_genomic.fna.gz | prodigal -d GCF_007097205.2_ASM709720v2_genomic.fna/cds.fna -a GCF_007097205.2_ASM709720v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:34,179] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:34,179] [INFO] Task started: HMMsearch
[2024-01-25 20:02:34,179] [INFO] Running command: hmmsearch --tblout GCF_007097205.2_ASM709720v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference/reference_markers.hmm GCF_007097205.2_ASM709720v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:34,498] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:34,499] [INFO] Found 6/6 markers.
[2024-01-25 20:02:34,545] [INFO] Query marker FASTA was written to GCF_007097205.2_ASM709720v2_genomic.fna/markers.fasta
[2024-01-25 20:02:34,546] [INFO] Task started: Blastn
[2024-01-25 20:02:34,546] [INFO] Running command: blastn -query GCF_007097205.2_ASM709720v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference/reference_markers.fasta -out GCF_007097205.2_ASM709720v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:35,870] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:35,873] [INFO] Selected 26 target genomes.
[2024-01-25 20:02:35,873] [INFO] Target genome list was writen to GCF_007097205.2_ASM709720v2_genomic.fna/target_genomes.txt
[2024-01-25 20:02:35,886] [INFO] Task started: fastANI
[2024-01-25 20:02:35,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd243361-347b-454a-938a-70749a87c028/GCF_007097205.2_ASM709720v2_genomic.fna.gz --refList GCF_007097205.2_ASM709720v2_genomic.fna/target_genomes.txt --output GCF_007097205.2_ASM709720v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:08,984] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:08,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:08,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:08,998] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:08,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:08,999] [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 alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	100.0	1625	1648	95	conclusive
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	92.6482	1155	1648	95	below_threshold
Streptomyces tardus	strain=P38-E01	GCA_018101125.2	2780544	2780544	type	True	82.0915	934	1648	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	81.6648	927	1648	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	81.4783	876	1648	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	81.338	813	1648	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	81.1808	639	1648	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	81.1185	833	1648	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	81.0334	875	1648	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	81.0029	769	1648	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.8333	884	1648	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	80.7274	832	1648	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	80.6776	799	1648	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	80.6631	769	1648	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	80.5962	771	1648	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.577	892	1648	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	80.5663	730	1648	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.3829	808	1648	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	80.3743	819	1648	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	80.0344	885	1648	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.9718	900	1648	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	76.4637	326	1648	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	76.4059	335	1648	95	below_threshold
Actinoalloteichus cyanogriseus	strain=DSM 43889	GCA_000429185.2	65497	65497	type	True	76.1922	316	1648	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	76.0354	177	1648	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	75.9968	180	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:09,000] [INFO] DFAST Taxonomy check result was written to GCF_007097205.2_ASM709720v2_genomic.fna/tc_result.tsv
[2024-01-25 20:03:09,001] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:09,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:09,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference/checkm_data
[2024-01-25 20:03:09,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:09,059] [INFO] Task started: CheckM
[2024-01-25 20:03:09,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097205.2_ASM709720v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097205.2_ASM709720v2_genomic.fna/checkm_input GCF_007097205.2_ASM709720v2_genomic.fna/checkm_result
[2024-01-25 20:03:54,324] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:54,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:54,348] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:54,349] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:54,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097205.2_ASM709720v2_genomic.fna/markers.fasta)
[2024-01-25 20:03:54,349] [INFO] Task started: Blastn
[2024-01-25 20:03:54,349] [INFO] Running command: blastn -query GCF_007097205.2_ASM709720v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bc23e45-7362-4b08-abd7-4cf0fa015285/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097205.2_ASM709720v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:56,468] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:56,471] [INFO] Selected 29 target genomes.
[2024-01-25 20:03:56,471] [INFO] Target genome list was writen to GCF_007097205.2_ASM709720v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:56,495] [INFO] Task started: fastANI
[2024-01-25 20:03:56,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd243361-347b-454a-938a-70749a87c028/GCF_007097205.2_ASM709720v2_genomic.fna.gz --refList GCF_007097205.2_ASM709720v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007097205.2_ASM709720v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:39,912] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:39,930] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:39,930] [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_007097205.2	s__Streptomyces alkaliterrae	100.0	1625	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	conclusive
GCF_018101125.2	s__Streptomyces sp018101125	82.1196	930	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779715.1	s__Streptomyces chumphonensis	81.6795	926	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	81.6085	850	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_000424845.1	s__Streptomyces sp000424845	81.4674	833	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	81.4637	879	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_900110735.1	s__Streptomyces radiopugnans	81.4567	888	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	81.4199	802	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418495.1	s__Streptomyces pathocidini	81.1926	638	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	81.1163	851	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	81.0701	869	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	81.0632	764	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280575.1	s__Streptomyces sp007280575	80.8995	743	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	80.8589	817	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	80.7488	829	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_004784465.1	s__Streptomyces griseoluteus	80.6437	765	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_004784475.1	s__Streptomyces bauhiniae	80.6429	763	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	95.70	95.47	0.88	0.84	6	-
GCF_000720725.1	s__Streptomyces rimosus_A	80.6147	858	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090105.1	s__Streptomyces sp019090105	80.5976	766	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654895.1	s__Streptomyces filamentosus	80.5625	886	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_013302895.1	s__Streptomyces chlorinus	80.5155	865	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927245.1	s__Streptomyces sp012927245	80.4616	889	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905845.1	s__Streptomyces sp001905845	80.3871	905	1648	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	80.2758	846	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_014203595.1	s__Streptomyces echinatus	80.1751	861	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755605.1	s__Streptomyces typhae	80.1028	842	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.66	98.66	0.93	0.93	2	-
GCF_000968685.2	s__Streptomyces antioxidans	80.1012	803	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495685.1	s__Streptomyces sp014495685	80.0464	794	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	79.7094	849	1648	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 20:04:39,932] [INFO] GTDB search result was written to GCF_007097205.2_ASM709720v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:39,932] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:39,938] [INFO] DFAST_QC result json was written to GCF_007097205.2_ASM709720v2_genomic.fna/dqc_result.json
[2024-01-25 20:04:39,938] [INFO] DFAST_QC completed!
[2024-01-25 20:04:39,939] [INFO] Total running time: 0h2m19s