[2024-01-24 12:44:11,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,058] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference
[2024-01-24 12:44:12,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,427] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b343e6-6dff-41ec-99c2-2c4ed8245fc1/GCF_004348415.1_ASM434841v1_genomic.fna.gz | prodigal -d GCF_004348415.1_ASM434841v1_genomic.fna/cds.fna -a GCF_004348415.1_ASM434841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:30,935] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:30,935] [INFO] Task started: HMMsearch
[2024-01-24 12:44:30,935] [INFO] Running command: hmmsearch --tblout GCF_004348415.1_ASM434841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference/reference_markers.hmm GCF_004348415.1_ASM434841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:31,367] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:31,369] [INFO] Found 6/6 markers.
[2024-01-24 12:44:31,438] [INFO] Query marker FASTA was written to GCF_004348415.1_ASM434841v1_genomic.fna/markers.fasta
[2024-01-24 12:44:31,439] [INFO] Task started: Blastn
[2024-01-24 12:44:31,439] [INFO] Running command: blastn -query GCF_004348415.1_ASM434841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference/reference_markers.fasta -out GCF_004348415.1_ASM434841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:32,787] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:32,790] [INFO] Selected 16 target genomes.
[2024-01-24 12:44:32,791] [INFO] Target genome list was writen to GCF_004348415.1_ASM434841v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:32,799] [INFO] Task started: fastANI
[2024-01-24 12:44:32,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b343e6-6dff-41ec-99c2-2c4ed8245fc1/GCF_004348415.1_ASM434841v1_genomic.fna.gz --refList GCF_004348415.1_ASM434841v1_genomic.fna/target_genomes.txt --output GCF_004348415.1_ASM434841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:00,343] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:00,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:00,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:00,358] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:00,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:00,359] [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 hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	100.0	2161	2201	95	conclusive
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	81.7777	1177	2201	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.7719	974	2201	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	81.5759	1042	2201	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	81.4108	1172	2201	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	81.4052	1193	2201	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	81.3169	1137	2201	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	81.3028	1079	2201	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	81.2151	1104	2201	95	below_threshold
Streptomyces xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	81.1453	1067	2201	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.1478	908	2201	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	78.988	789	2201	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	78.9865	872	2201	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	78.9769	884	2201	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	78.6287	997	2201	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	78.5058	983	2201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:00,361] [INFO] DFAST Taxonomy check result was written to GCF_004348415.1_ASM434841v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:00,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:00,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:00,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference/checkm_data
[2024-01-24 12:45:00,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:00,446] [INFO] Task started: CheckM
[2024-01-24 12:45:00,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348415.1_ASM434841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348415.1_ASM434841v1_genomic.fna/checkm_input GCF_004348415.1_ASM434841v1_genomic.fna/checkm_result
[2024-01-24 12:45:58,079] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:58,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:58,112] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:58,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:58,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348415.1_ASM434841v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:58,113] [INFO] Task started: Blastn
[2024-01-24 12:45:58,113] [INFO] Running command: blastn -query GCF_004348415.1_ASM434841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a9a0716-bb79-4e11-96de-72e3476f5278/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348415.1_ASM434841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:00,215] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:00,219] [INFO] Selected 16 target genomes.
[2024-01-24 12:46:00,220] [INFO] Target genome list was writen to GCF_004348415.1_ASM434841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:00,239] [INFO] Task started: fastANI
[2024-01-24 12:46:00,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b343e6-6dff-41ec-99c2-2c4ed8245fc1/GCF_004348415.1_ASM434841v1_genomic.fna.gz --refList GCF_004348415.1_ASM434841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348415.1_ASM434841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:28,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:28,517] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:28,517] [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_004348415.1	s__Streptomyces hainanensis	100.0	2161	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004348315.1	s__Streptomyces sp004348315	87.7418	1455	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083795.1	s__Streptomyces sp001083795	81.7856	1106	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626535.1	s__Streptomyces hoynatensis	81.7791	1177	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.7569	976	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696235.1	s__Streptomyces triticirhizae	81.5499	1047	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_001984575.1	s__Streptomyces sp001984575	81.5236	1198	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626575.1	s__Streptomyces sp003626575	81.4186	1171	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002128305.1	s__Streptomyces sp002128305	81.3834	1094	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719135.1	s__Streptomyces avicenniae	81.2534	1102	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	81.246	1098	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116145.1	s__Streptomyces harbinensis	81.2304	1066	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	-
GCF_000993785.3	s__Streptomyces xiamenensis	81.152	1066	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	97.97	0.94	0.91	3	-
GCF_004193175.1	s__Streptomyces sp004193175	81.048	1073	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974485.1	s__Streptomyces sp000974485	80.7181	1148	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	78.98	981	2201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:28,519] [INFO] GTDB search result was written to GCF_004348415.1_ASM434841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:28,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:28,523] [INFO] DFAST_QC result json was written to GCF_004348415.1_ASM434841v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:28,523] [INFO] DFAST_QC completed!
[2024-01-24 12:46:28,524] [INFO] Total running time: 0h2m17s