[2024-01-24 13:10:03,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference
[2024-01-24 13:10:05,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,071] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg36c7f835-8bf9-4f1b-974c-e0ec7210f4a4/GCF_007280575.1_ASM728057v1_genomic.fna.gz | prodigal -d GCF_007280575.1_ASM728057v1_genomic.fna/cds.fna -a GCF_007280575.1_ASM728057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:24,089] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:24,089] [INFO] Task started: HMMsearch
[2024-01-24 13:10:24,090] [INFO] Running command: hmmsearch --tblout GCF_007280575.1_ASM728057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference/reference_markers.hmm GCF_007280575.1_ASM728057v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:24,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:24,478] [INFO] Found 6/6 markers.
[2024-01-24 13:10:24,538] [INFO] Query marker FASTA was written to GCF_007280575.1_ASM728057v1_genomic.fna/markers.fasta
[2024-01-24 13:10:24,538] [INFO] Task started: Blastn
[2024-01-24 13:10:24,538] [INFO] Running command: blastn -query GCF_007280575.1_ASM728057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference/reference_markers.fasta -out GCF_007280575.1_ASM728057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:25,904] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:25,911] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:25,912] [INFO] Target genome list was writen to GCF_007280575.1_ASM728057v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:25,920] [INFO] Task started: fastANI
[2024-01-24 13:10:25,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg36c7f835-8bf9-4f1b-974c-e0ec7210f4a4/GCF_007280575.1_ASM728057v1_genomic.fna.gz --refList GCF_007280575.1_ASM728057v1_genomic.fna/target_genomes.txt --output GCF_007280575.1_ASM728057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:02,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:02,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:02,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:02,478] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:11:02,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:11:02,479] [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 benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	100.0	1927	1950	95	conclusive
Streptomyces catenulae	strain=NRRL B-2342	GCA_000718015.1	66875	66875	type	True	92.7706	1541	1950	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	86.2916	1404	1950	95	below_threshold
Streptomyces angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	84.8502	1081	1950	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	84.8148	1299	1950	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	84.7728	1306	1950	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	84.7469	1233	1950	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	84.6585	1288	1950	95	below_threshold
Streptomyces lydicus	strain=NRRL ISP-5461	GCA_000717345.1	47763	47763	suspected-type	True	84.5915	1290	1950	95	below_threshold
Streptomyces lydicus	strain=ATCC 25470	GCA_004125245.1	47763	47763	suspected-type	True	84.5884	1288	1950	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	84.5799	1253	1950	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	84.5493	1217	1950	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	84.528	1241	1950	95	below_threshold
Streptomyces piniterrae	strain=jys28	GCA_005048155.1	2571125	2571125	type	True	84.4852	1241	1950	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	84.4068	1269	1950	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.4431	1238	1950	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.4406	1217	1950	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.3749	1217	1950	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	82.0249	1002	1950	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	81.6433	991	1950	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	81.3812	1022	1950	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	81.329	1045	1950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:02,480] [INFO] DFAST Taxonomy check result was written to GCF_007280575.1_ASM728057v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:02,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:02,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:02,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference/checkm_data
[2024-01-24 13:11:02,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:02,546] [INFO] Task started: CheckM
[2024-01-24 13:11:02,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007280575.1_ASM728057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007280575.1_ASM728057v1_genomic.fna/checkm_input GCF_007280575.1_ASM728057v1_genomic.fna/checkm_result
[2024-01-24 13:12:03,348] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:03,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:03,380] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:03,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:03,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007280575.1_ASM728057v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:03,381] [INFO] Task started: Blastn
[2024-01-24 13:12:03,381] [INFO] Running command: blastn -query GCF_007280575.1_ASM728057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e29879-bec7-4892-bf47-a7bbcd53fab5/dqc_reference/reference_markers_gtdb.fasta -out GCF_007280575.1_ASM728057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:05,465] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:05,470] [INFO] Selected 21 target genomes.
[2024-01-24 13:12:05,470] [INFO] Target genome list was writen to GCF_007280575.1_ASM728057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:05,598] [INFO] Task started: fastANI
[2024-01-24 13:12:05,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg36c7f835-8bf9-4f1b-974c-e0ec7210f4a4/GCF_007280575.1_ASM728057v1_genomic.fna.gz --refList GCF_007280575.1_ASM728057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007280575.1_ASM728057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:41,158] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:41,181] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:41,181] [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_007280575.1	s__Streptomyces sp007280575	100.0	1927	1950	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_000718015.1	s__Streptomyces catenulae	92.7579	1542	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720995.1	s__Streptomyces celluloflavus	84.8122	1285	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.24	98.62	0.95	0.89	4	-
GCF_014646275.1	s__Streptomyces kronopolitis	84.746	1232	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	84.6785	1285	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000717345.1	s__Streptomyces lydicus	84.5727	1291	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.38	0.95	0.89	6	-
GCF_008704855.1	s__Streptomyces platensis	84.569	1274	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_009811635.1	s__Streptomyces tubercidicus	84.5258	1245	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122735.1	s__Streptomyces sioyaensis	84.5175	1222	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_005048155.1	s__Streptomyces piniterrae	84.4963	1240	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648695.1	s__Streptomyces albospinus	84.494	1245	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004125265.1	s__Streptomyces lydicus_C	84.4724	1252	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	84.4629	1266	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_003389455.1	s__Streptomyces inhibens	84.4373	1265	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805335.1	s__Streptomyces sp000805335	84.3934	1244	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	84.3336	1245	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_000935125.1	s__Streptomyces natalensis	84.2765	1233	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCA_000963515.1	s__Streptomyces albulus_C	84.1807	1319	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.74	99.39	0.98	0.95	6	-
GCF_000720725.1	s__Streptomyces rimosus_A	83.3227	1223	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650175.1	s__Streptomyces termitum	81.2761	1041	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719475.1	s__Streptomyces sp000719475	80.109	845	1950	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 13:12:41,183] [INFO] GTDB search result was written to GCF_007280575.1_ASM728057v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:41,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:41,188] [INFO] DFAST_QC result json was written to GCF_007280575.1_ASM728057v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:41,188] [INFO] DFAST_QC completed!
[2024-01-24 13:12:41,188] [INFO] Total running time: 0h2m37s