[2024-01-25 18:57:20,600] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:20,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:20,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference
[2024-01-25 18:57:21,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:21,775] [INFO] Task started: Prodigal
[2024-01-25 18:57:21,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg328ff880-e0a4-42bd-8ec8-447605fedb0c/GCF_009377185.1_ASM937718v1_genomic.fna.gz | prodigal -d GCF_009377185.1_ASM937718v1_genomic.fna/cds.fna -a GCF_009377185.1_ASM937718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:52,902] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:52,902] [INFO] Task started: HMMsearch
[2024-01-25 18:57:52,902] [INFO] Running command: hmmsearch --tblout GCF_009377185.1_ASM937718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference/reference_markers.hmm GCF_009377185.1_ASM937718v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:53,319] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:53,320] [INFO] Found 6/6 markers.
[2024-01-25 18:57:53,404] [INFO] Query marker FASTA was written to GCF_009377185.1_ASM937718v1_genomic.fna/markers.fasta
[2024-01-25 18:57:53,405] [INFO] Task started: Blastn
[2024-01-25 18:57:53,405] [INFO] Running command: blastn -query GCF_009377185.1_ASM937718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference/reference_markers.fasta -out GCF_009377185.1_ASM937718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:54,693] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:54,697] [INFO] Selected 19 target genomes.
[2024-01-25 18:57:54,697] [INFO] Target genome list was writen to GCF_009377185.1_ASM937718v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:54,708] [INFO] Task started: fastANI
[2024-01-25 18:57:54,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg328ff880-e0a4-42bd-8ec8-447605fedb0c/GCF_009377185.1_ASM937718v1_genomic.fna.gz --refList GCF_009377185.1_ASM937718v1_genomic.fna/target_genomes.txt --output GCF_009377185.1_ASM937718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:36,765] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:36,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:36,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:36,778] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:36,779] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:36,779] [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 spongiae	strain=NBRC 106415	GCA_009377185.1	565072	565072	type	True	100.0	3165	3207	95	conclusive
Streptomyces bluensis	strain=JCM 4729	GCA_014650715.1	33897	33897	type	True	89.8914	1867	3207	95	below_threshold
Streptomyces acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	89.8467	1881	3207	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	88.1907	1781	3207	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	85.0192	1773	3207	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	84.9058	1527	3207	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.8706	1878	3207	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	84.8676	1359	3207	95	below_threshold
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	84.7468	1473	3207	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	84.6372	1758	3207	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	84.6238	1646	3207	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.3344	1518	3207	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	84.258	1745	3207	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.2563	1835	3207	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	84.0843	1546	3207	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	83.9216	1635	3207	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.7438	1522	3207	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.5329	1416	3207	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.5236	1664	3207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:36,780] [INFO] DFAST Taxonomy check result was written to GCF_009377185.1_ASM937718v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:36,780] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:36,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:36,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference/checkm_data
[2024-01-25 18:58:36,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:36,882] [INFO] Task started: CheckM
[2024-01-25 18:58:36,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009377185.1_ASM937718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009377185.1_ASM937718v1_genomic.fna/checkm_input GCF_009377185.1_ASM937718v1_genomic.fna/checkm_result
[2024-01-25 19:00:38,114] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:38,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:38,144] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:38,144] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:38,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009377185.1_ASM937718v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:38,146] [INFO] Task started: Blastn
[2024-01-25 19:00:38,146] [INFO] Running command: blastn -query GCF_009377185.1_ASM937718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55de2fc3-987b-4a19-8405-4684a60031bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009377185.1_ASM937718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:40,440] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:40,443] [INFO] Selected 20 target genomes.
[2024-01-25 19:00:40,443] [INFO] Target genome list was writen to GCF_009377185.1_ASM937718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:40,473] [INFO] Task started: fastANI
[2024-01-25 19:00:40,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg328ff880-e0a4-42bd-8ec8-447605fedb0c/GCF_009377185.1_ASM937718v1_genomic.fna.gz --refList GCF_009377185.1_ASM937718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009377185.1_ASM937718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:25,363] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:25,376] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:01:25,376] [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_009377235.1	s__Streptomyces acidicola	89.8677	1878	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.86	96.86	0.86	0.86	2	-
GCF_014650715.1	s__Streptomyces bluensis	89.8586	1871	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.08	99.08	0.92	0.92	2	-
GCF_009377205.1	s__Streptomyces phyllanthi	88.1912	1782	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386495.1	s__Streptomyces tailanensis	85.0375	1769	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598475.1	s__Streptomyces adelaidensis	84.9687	1741	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214185.1	s__Streptomyces capitiformicae	84.9009	1810	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	-
GCF_001418645.1	s__Streptomyces neyagawaensis	84.8844	1359	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_014648075.1	s__Streptomyces ruber	84.7753	1469	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	84.6154	1649	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCA_000415505.1	s__Streptomyces afghaniensis	84.5311	1666	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	84.4917	1897	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	84.3943	1850	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	84.3399	1730	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016598615.1	s__Streptomyces sp016598615	84.2866	1907	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.2682	1798	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	84.2638	1745	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_014202475.1	s__Streptomyces paradoxus	84.2051	1657	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	83.9132	1637	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_007176755.1	s__Streptomyces sp007176755	83.2752	1406	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	83.0237	1557	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:25,378] [INFO] GTDB search result was written to GCF_009377185.1_ASM937718v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:25,378] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:25,382] [INFO] DFAST_QC result json was written to GCF_009377185.1_ASM937718v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:25,382] [INFO] DFAST_QC completed!
[2024-01-25 19:01:25,382] [INFO] Total running time: 0h4m5s