[2024-01-25 17:58:35,437] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,439] [INFO] DQC Reference Directory: /var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference
[2024-01-25 17:58:36,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,545] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg4863c239-519d-4403-beac-d0baf200bbc6/GCF_000716545.1_ASM71654v1_genomic.fna.gz | prodigal -d GCF_000716545.1_ASM71654v1_genomic.fna/cds.fna -a GCF_000716545.1_ASM71654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:53,102] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:53,103] [INFO] Task started: HMMsearch
[2024-01-25 17:58:53,103] [INFO] Running command: hmmsearch --tblout GCF_000716545.1_ASM71654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference/reference_markers.hmm GCF_000716545.1_ASM71654v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:53,423] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:53,424] [INFO] Found 6/6 markers.
[2024-01-25 17:58:53,487] [INFO] Query marker FASTA was written to GCF_000716545.1_ASM71654v1_genomic.fna/markers.fasta
[2024-01-25 17:58:53,487] [INFO] Task started: Blastn
[2024-01-25 17:58:53,487] [INFO] Running command: blastn -query GCF_000716545.1_ASM71654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference/reference_markers.fasta -out GCF_000716545.1_ASM71654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:54,820] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:54,823] [INFO] Selected 11 target genomes.
[2024-01-25 17:58:54,823] [INFO] Target genome list was writen to GCF_000716545.1_ASM71654v1_genomic.fna/target_genomes.txt
[2024-01-25 17:58:54,833] [INFO] Task started: fastANI
[2024-01-25 17:58:54,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg4863c239-519d-4403-beac-d0baf200bbc6/GCF_000716545.1_ASM71654v1_genomic.fna.gz --refList GCF_000716545.1_ASM71654v1_genomic.fna/target_genomes.txt --output GCF_000716545.1_ASM71654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:21,651] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:21,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:21,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:21,660] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:59:21,660] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:21,660] [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 phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	100.0	2444	2451	95	conclusive
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	91.236	1870	2451	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	91.1981	1930	2451	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	88.4867	1806	2451	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	88.1834	1731	2451	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	84.4836	1578	2451	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	83.1731	1446	2451	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	82.7518	1560	2451	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.1972	1292	2451	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.3022	1138	2451	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.1544	938	2451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:21,661] [INFO] DFAST Taxonomy check result was written to GCF_000716545.1_ASM71654v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:21,663] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:21,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:21,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference/checkm_data
[2024-01-25 17:59:21,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:21,746] [INFO] Task started: CheckM
[2024-01-25 17:59:21,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000716545.1_ASM71654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000716545.1_ASM71654v1_genomic.fna/checkm_input GCF_000716545.1_ASM71654v1_genomic.fna/checkm_result
[2024-01-25 18:00:54,399] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:54,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:54,420] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:54,420] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:54,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000716545.1_ASM71654v1_genomic.fna/markers.fasta)
[2024-01-25 18:00:54,421] [INFO] Task started: Blastn
[2024-01-25 18:00:54,421] [INFO] Running command: blastn -query GCF_000716545.1_ASM71654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge425a7c7-390f-4b8e-bb91-5f154e0c556b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000716545.1_ASM71654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:56,720] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:56,722] [INFO] Selected 9 target genomes.
[2024-01-25 18:00:56,722] [INFO] Target genome list was writen to GCF_000716545.1_ASM71654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:56,732] [INFO] Task started: fastANI
[2024-01-25 18:00:56,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg4863c239-519d-4403-beac-d0baf200bbc6/GCF_000716545.1_ASM71654v1_genomic.fna.gz --refList GCF_000716545.1_ASM71654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000716545.1_ASM71654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:22,855] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:22,862] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:22,862] [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_000716545.1	s__Kitasatospora phosalacinea	100.0	2444	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013364235.1	s__Kitasatospora sp013364235	93.684	2000	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	92.7442	1975	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751605.1	s__Kitasatospora cineracea	92.0294	2043	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.58	96.37	0.89	0.86	4	-
GCF_002813165.1	s__Kitasatospora sp002813165	91.6159	1928	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.28	97.28	0.90	0.90	2	-
GCF_000269985.1	s__Kitasatospora setae	91.1997	1930	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.99	99.98	0.99	0.99	3	-
GCF_002754615.1	s__Kitasatospora sp002754615	89.2213	1948	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014648555.1	s__Kitasatospora griseola	88.2109	1728	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.80	97.68	0.89	0.89	3	-
GCF_001905465.1	s__Kitasatospora sp001905465	88.1324	1721	2451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:22,863] [INFO] GTDB search result was written to GCF_000716545.1_ASM71654v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:22,864] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:22,867] [INFO] DFAST_QC result json was written to GCF_000716545.1_ASM71654v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:22,867] [INFO] DFAST_QC completed!
[2024-01-25 18:01:22,867] [INFO] Total running time: 0h2m47s