[2024-01-24 14:38:48,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:48,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:48,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference
[2024-01-24 14:38:50,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,450] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,451] [INFO] Running command: gunzip -c /var/lib/cwl/stged581686-8024-4171-9aad-03db7c97757f/GCF_008806595.1_ASM880659v1_genomic.fna.gz | prodigal -d GCF_008806595.1_ASM880659v1_genomic.fna/cds.fna -a GCF_008806595.1_ASM880659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:19,628] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:19,628] [INFO] Task started: HMMsearch
[2024-01-24 14:39:19,629] [INFO] Running command: hmmsearch --tblout GCF_008806595.1_ASM880659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference/reference_markers.hmm GCF_008806595.1_ASM880659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:20,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:20,153] [INFO] Found 6/6 markers.
[2024-01-24 14:39:20,229] [INFO] Query marker FASTA was written to GCF_008806595.1_ASM880659v1_genomic.fna/markers.fasta
[2024-01-24 14:39:20,229] [INFO] Task started: Blastn
[2024-01-24 14:39:20,229] [INFO] Running command: blastn -query GCF_008806595.1_ASM880659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference/reference_markers.fasta -out GCF_008806595.1_ASM880659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:21,740] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:21,743] [INFO] Selected 26 target genomes.
[2024-01-24 14:39:21,744] [INFO] Target genome list was writen to GCF_008806595.1_ASM880659v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:21,754] [INFO] Task started: fastANI
[2024-01-24 14:39:21,755] [INFO] Running command: fastANI --query /var/lib/cwl/stged581686-8024-4171-9aad-03db7c97757f/GCF_008806595.1_ASM880659v1_genomic.fna.gz --refList GCF_008806595.1_ASM880659v1_genomic.fna/target_genomes.txt --output GCF_008806595.1_ASM880659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:17,766] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:17,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:17,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:17,788] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:17,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:17,789] [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 curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	86.5169	1741	2963	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	85.9754	1940	2963	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.7974	1676	2963	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.795	1737	2963	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.7804	1847	2963	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	85.7761	1735	2963	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.7334	1764	2963	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.6903	1699	2963	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.6522	1825	2963	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	85.6258	1757	2963	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	85.5974	1721	2963	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.584	1762	2963	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.5281	1681	2963	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.3042	1781	2963	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	85.2766	1630	2963	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.2715	1634	2963	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.1768	1459	2963	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.122	1357	2963	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	85.1083	1324	2963	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	85.0342	1672	2963	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	85.0254	1791	2963	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	84.9982	1778	2963	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.8133	1594	2963	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.7189	1347	2963	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	84.5372	1719	2963	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	84.2468	1367	2963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:17,790] [INFO] DFAST Taxonomy check result was written to GCF_008806595.1_ASM880659v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:17,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:17,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:17,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference/checkm_data
[2024-01-24 14:40:17,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:17,874] [INFO] Task started: CheckM
[2024-01-24 14:40:17,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008806595.1_ASM880659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008806595.1_ASM880659v1_genomic.fna/checkm_input GCF_008806595.1_ASM880659v1_genomic.fna/checkm_result
[2024-01-24 14:41:59,938] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:59,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:41:59,987] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:59,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:59,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008806595.1_ASM880659v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:59,989] [INFO] Task started: Blastn
[2024-01-24 14:41:59,989] [INFO] Running command: blastn -query GCF_008806595.1_ASM880659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d1484b-6a08-4c49-a580-fd05d77784c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008806595.1_ASM880659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:02,344] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:02,348] [INFO] Selected 25 target genomes.
[2024-01-24 14:42:02,348] [INFO] Target genome list was writen to GCF_008806595.1_ASM880659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:02,372] [INFO] Task started: fastANI
[2024-01-24 14:42:02,373] [INFO] Running command: fastANI --query /var/lib/cwl/stged581686-8024-4171-9aad-03db7c97757f/GCF_008806595.1_ASM880659v1_genomic.fna.gz --refList GCF_008806595.1_ASM880659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008806595.1_ASM880659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:01,111] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:01,131] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:01,132] [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_009827025.1	s__Streptomyces sp009827025	97.6932	2486	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.69	97.69	0.89	0.89	2	conclusive
GCF_002291145.1	s__Streptomyces sp002291145	86.7963	1756	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279775.1	s__Streptomyces sp001279775	86.7382	1842	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851625.1	s__Streptomyces sp003851625	86.536	1823	2963	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	86.3943	1817	2963	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	86.2483	1707	2963	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	86.1616	1848	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	86.028	1838	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004187715.1	s__Streptomyces sp004187715	85.9646	1762	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411315.1	s__Streptomyces sp000411315	85.8649	1765	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	85.831	1723	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270495.1	s__Streptomyces viridochromogenes_A	85.8175	1797	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCF_019049285.1	s__Streptomyces sp019049285	85.7226	1774	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	85.6797	1819	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	85.6127	1719	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_014203535.1	s__Streptomyces griseostramineus	85.274	1633	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_011193355.1	s__Streptomyces sp011193355	85.2703	1565	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091315.1	s__Streptomyces sp900091315	85.2448	1696	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688995.1	s__Streptomyces shenzhenensis	85.0074	1679	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	84.9809	1582	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	84.7724	1601	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548465.1	s__Streptomyces sp010548465	84.6869	1255	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	84.2937	1583	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_000829695.1	s__Streptomyces sp000829695	84.1154	1519	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.65	99.65	0.91	0.91	2	-
GCF_000317595.1	s__Streptomyces ipomoeae	84.0285	1571	2963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:01,134] [INFO] GTDB search result was written to GCF_008806595.1_ASM880659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:01,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:01,140] [INFO] DFAST_QC result json was written to GCF_008806595.1_ASM880659v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:01,140] [INFO] DFAST_QC completed!
[2024-01-24 14:43:01,141] [INFO] Total running time: 0h4m13s