[2024-01-24 13:55:40,897] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:40,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:40,900] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference
[2024-01-24 13:55:42,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,359] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg467d8b94-c894-4e96-92bf-7bd6b808a4b8/GCF_009377235.1_ASM937723v1_genomic.fna.gz | prodigal -d GCF_009377235.1_ASM937723v1_genomic.fna/cds.fna -a GCF_009377235.1_ASM937723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:14,438] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:14,439] [INFO] Task started: HMMsearch
[2024-01-24 13:56:14,439] [INFO] Running command: hmmsearch --tblout GCF_009377235.1_ASM937723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference/reference_markers.hmm GCF_009377235.1_ASM937723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:14,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:14,841] [INFO] Found 6/6 markers.
[2024-01-24 13:56:14,920] [INFO] Query marker FASTA was written to GCF_009377235.1_ASM937723v1_genomic.fna/markers.fasta
[2024-01-24 13:56:14,920] [INFO] Task started: Blastn
[2024-01-24 13:56:14,921] [INFO] Running command: blastn -query GCF_009377235.1_ASM937723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference/reference_markers.fasta -out GCF_009377235.1_ASM937723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:16,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:16,190] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:16,191] [INFO] Target genome list was writen to GCF_009377235.1_ASM937723v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:16,205] [INFO] Task started: fastANI
[2024-01-24 13:56:16,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg467d8b94-c894-4e96-92bf-7bd6b808a4b8/GCF_009377235.1_ASM937723v1_genomic.fna.gz --refList GCF_009377235.1_ASM937723v1_genomic.fna/target_genomes.txt --output GCF_009377235.1_ASM937723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:01,685] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:01,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:01,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:01,703] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:01,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:01,704] [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 acidicola	strain=K1PN6	GCA_009377235.1	2596892	2596892	type	True	100.0	3113	3155	95	conclusive
Streptomyces bluensis	strain=JCM 4729	GCA_014650715.1	33897	33897	type	True	93.7029	2245	3155	95	below_threshold
Streptomyces spongiae	strain=NBRC 106415	GCA_009377185.1	565072	565072	type	True	89.9259	1856	3155	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	87.7897	1684	3155	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	84.5544	1810	3155	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	84.4935	1752	3155	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	84.4778	1690	3155	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	84.3474	1845	3155	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	84.167	1721	3155	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	84.1414	1803	3155	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	84.072	1924	3155	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.0315	1613	3155	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	83.9849	1817	3155	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.8127	1564	3155	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.8107	1798	3155	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.7215	1476	3155	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	83.3404	1487	3155	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	83.3132	1440	3155	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	83.2979	1691	3155	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	82.9782	1563	3155	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	82.896	1631	3155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:01,705] [INFO] DFAST Taxonomy check result was written to GCF_009377235.1_ASM937723v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:01,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:01,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:01,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference/checkm_data
[2024-01-24 13:57:01,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:01,802] [INFO] Task started: CheckM
[2024-01-24 13:57:01,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009377235.1_ASM937723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009377235.1_ASM937723v1_genomic.fna/checkm_input GCF_009377235.1_ASM937723v1_genomic.fna/checkm_result
[2024-01-24 13:58:53,319] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:53,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,346] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:53,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:53,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009377235.1_ASM937723v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:53,347] [INFO] Task started: Blastn
[2024-01-24 13:58:53,347] [INFO] Running command: blastn -query GCF_009377235.1_ASM937723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a927ca-1203-436c-abc7-4f917450ee9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009377235.1_ASM937723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:55,465] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:55,473] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:55,474] [INFO] Target genome list was writen to GCF_009377235.1_ASM937723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:55,489] [INFO] Task started: fastANI
[2024-01-24 13:58:55,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg467d8b94-c894-4e96-92bf-7bd6b808a4b8/GCF_009377235.1_ASM937723v1_genomic.fna.gz --refList GCF_009377235.1_ASM937723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009377235.1_ASM937723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:41,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:41,302] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:41,302] [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	100.0	3110	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.86	96.86	0.86	0.86	2	conclusive
GCF_014650715.1	s__Streptomyces bluensis	93.7075	2244	3155	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	87.7939	1682	3155	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	84.6584	1821	3155	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	84.5674	1345	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	84.4997	1828	3155	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	84.464	1693	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_900290235.1	s__Streptomyces sp900290235	84.3692	1794	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	96.28	96.28	0.86	0.86	2	-
GCF_008905045.1	s__Streptomyces albicerus	84.287	1878	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	84.2279	1888	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091305.1	s__Streptomyces scabiei	84.2203	1761	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	97.09	0.94	0.86	16	-
GCF_015160855.1	s__Streptomyces ferrugineus	84.1742	1796	3155	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	84.1531	1750	3155	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	84.027	1922	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509475.1	s__Streptomyces regalis	84.0022	1812	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	83.942	1826	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	83.6351	1763	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	83.3673	1483	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006540305.1	s__Streptomyces sp006540305	83.3501	1556	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803075.1	s__Streptomyces sp002803075	83.3112	1482	3155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:41,304] [INFO] GTDB search result was written to GCF_009377235.1_ASM937723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:41,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:41,309] [INFO] DFAST_QC result json was written to GCF_009377235.1_ASM937723v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:41,309] [INFO] DFAST_QC completed!
[2024-01-24 13:59:41,309] [INFO] Total running time: 0h4m0s