[2024-01-24 13:55:47,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:47,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:47,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference
[2024-01-24 13:55:49,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,010] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,011] [INFO] Running command: gunzip -c /var/lib/cwl/stge0667925-53b6-405c-8d23-8ecc7b591fc5/GCF_020907985.1_ASM2090798v1_genomic.fna.gz | prodigal -d GCF_020907985.1_ASM2090798v1_genomic.fna/cds.fna -a GCF_020907985.1_ASM2090798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:15,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:15,142] [INFO] Task started: HMMsearch
[2024-01-24 13:56:15,142] [INFO] Running command: hmmsearch --tblout GCF_020907985.1_ASM2090798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference/reference_markers.hmm GCF_020907985.1_ASM2090798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:15,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:15,515] [INFO] Found 6/6 markers.
[2024-01-24 13:56:15,580] [INFO] Query marker FASTA was written to GCF_020907985.1_ASM2090798v1_genomic.fna/markers.fasta
[2024-01-24 13:56:15,581] [INFO] Task started: Blastn
[2024-01-24 13:56:15,581] [INFO] Running command: blastn -query GCF_020907985.1_ASM2090798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference/reference_markers.fasta -out GCF_020907985.1_ASM2090798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:16,982] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:16,985] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:16,985] [INFO] Target genome list was writen to GCF_020907985.1_ASM2090798v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:16,997] [INFO] Task started: fastANI
[2024-01-24 13:56:16,997] [INFO] Running command: fastANI --query /var/lib/cwl/stge0667925-53b6-405c-8d23-8ecc7b591fc5/GCF_020907985.1_ASM2090798v1_genomic.fna.gz --refList GCF_020907985.1_ASM2090798v1_genomic.fna/target_genomes.txt --output GCF_020907985.1_ASM2090798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:51,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:51,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:51,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:51,607] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:51,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:51,607] [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
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	100.0	2618	2621	95	conclusive
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	91.6474	1933	2621	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	85.9988	1749	2621	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	85.6256	1542	2621	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	84.6092	1573	2621	95	below_threshold
Kitasatospora mediocidica	strain=KCTC 9733	GCA_000744225.1	58352	58352	type	True	83.5849	1464	2621	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	82.6358	1376	2621	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	82.2469	1384	2621	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	82.1571	1288	2621	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	82.1385	1318	2621	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	79.9594	1140	2621	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	79.8148	1156	2621	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	79.5414	955	2621	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.5299	948	2621	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	78.9597	1006	2621	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.6009	1021	2621	95	below_threshold
Streptomyces xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	78.4761	768	2621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:51,611] [INFO] DFAST Taxonomy check result was written to GCF_020907985.1_ASM2090798v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:51,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:51,612] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:51,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference/checkm_data
[2024-01-24 13:56:51,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:51,698] [INFO] Task started: CheckM
[2024-01-24 13:56:51,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020907985.1_ASM2090798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020907985.1_ASM2090798v1_genomic.fna/checkm_input GCF_020907985.1_ASM2090798v1_genomic.fna/checkm_result
[2024-01-24 13:58:21,338] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:21,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,363] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:21,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:21,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020907985.1_ASM2090798v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:21,365] [INFO] Task started: Blastn
[2024-01-24 13:58:21,365] [INFO] Running command: blastn -query GCF_020907985.1_ASM2090798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18a4ab1b-a9bd-4d57-88d8-f849535c136c/dqc_reference/reference_markers_gtdb.fasta -out GCF_020907985.1_ASM2090798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:23,843] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:23,847] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:23,847] [INFO] Target genome list was writen to GCF_020907985.1_ASM2090798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:23,872] [INFO] Task started: fastANI
[2024-01-24 13:58:23,872] [INFO] Running command: fastANI --query /var/lib/cwl/stge0667925-53b6-405c-8d23-8ecc7b591fc5/GCF_020907985.1_ASM2090798v1_genomic.fna.gz --refList GCF_020907985.1_ASM2090798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020907985.1_ASM2090798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:56,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:56,352] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:56,353] [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_002846355.1	s__Kitasatospora sp002846355	91.2572	1964	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.05	96.05	0.83	0.83	2	-
GCF_007829815.1	s__Kitasatospora viridis	86.0079	1748	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744785.1	s__Kitasatospora azatica	85.6046	1545	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205575.1	s__Kitasatospora tateyamensis	85.2656	1441	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203855.1	s__Kitasatospora kifunensis	84.5572	1581	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744225.1	s__Kitasatospora mediocidica	83.6036	1461	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648975.1	s__Kitasatospora herbaricolor	82.2827	1382	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.20	96.20	0.86	0.86	2	-
GCF_014655955.1	s__Kitasatospora indigofera	82.0707	1397	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000269985.1	s__Kitasatospora setae	82.0678	1330	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.99	99.98	0.99	0.99	3	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	82.0446	1270	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813165.1	s__Kitasatospora sp002813165	82.0184	1339	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.28	97.28	0.90	0.90	2	-
GCF_014084105.1	s__Streptacidiphilus sp014084105	80.3888	1152	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744815.1	s__Streptacidiphilus_A oryzae	79.7431	1084	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112845.1	s__Streptomyces alni	78.9707	1001	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000993785.3	s__Streptomyces xiamenensis	78.4907	766	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	97.97	0.94	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,354] [INFO] GTDB search result was written to GCF_020907985.1_ASM2090798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:56,355] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:56,359] [INFO] DFAST_QC result json was written to GCF_020907985.1_ASM2090798v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:56,359] [INFO] DFAST_QC completed!
[2024-01-24 13:58:56,359] [INFO] Total running time: 0h3m9s