[2024-01-25 18:46:05,710] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:05,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:05,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference
[2024-01-25 18:46:06,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:06,845] [INFO] Task started: Prodigal
[2024-01-25 18:46:06,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb92987e-4612-4e5c-a5a0-20cecf2337aa/GCF_014655855.1_ASM1465585v1_genomic.fna.gz | prodigal -d GCF_014655855.1_ASM1465585v1_genomic.fna/cds.fna -a GCF_014655855.1_ASM1465585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:25,225] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:25,226] [INFO] Task started: HMMsearch
[2024-01-25 18:46:25,226] [INFO] Running command: hmmsearch --tblout GCF_014655855.1_ASM1465585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference/reference_markers.hmm GCF_014655855.1_ASM1465585v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:25,531] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:25,532] [INFO] Found 6/6 markers.
[2024-01-25 18:46:25,587] [INFO] Query marker FASTA was written to GCF_014655855.1_ASM1465585v1_genomic.fna/markers.fasta
[2024-01-25 18:46:25,588] [INFO] Task started: Blastn
[2024-01-25 18:46:25,588] [INFO] Running command: blastn -query GCF_014655855.1_ASM1465585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference/reference_markers.fasta -out GCF_014655855.1_ASM1465585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:26,737] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:26,741] [INFO] Selected 23 target genomes.
[2024-01-25 18:46:26,741] [INFO] Target genome list was writen to GCF_014655855.1_ASM1465585v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:26,755] [INFO] Task started: fastANI
[2024-01-25 18:46:26,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb92987e-4612-4e5c-a5a0-20cecf2337aa/GCF_014655855.1_ASM1465585v1_genomic.fna.gz --refList GCF_014655855.1_ASM1465585v1_genomic.fna/target_genomes.txt --output GCF_014655855.1_ASM1465585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:06,766] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:06,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:06,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:06,781] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:47:06,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:06,782] [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 candidus	strain=JCM 4629	GCA_014655855.1	67283	67283	type	True	100.0	2401	2401	95	conclusive
Streptomyces candidus	strain=DSM 40141	GCA_014207445.1	67283	67283	type	True	99.9936	2386	2401	95	conclusive
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	86.2384	1638	2401	95	below_threshold
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	83.3205	1056	2401	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	83.2382	1202	2401	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	82.967	1346	2401	95	below_threshold
Streptomyces flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	82.803	1341	2401	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	82.2912	1094	2401	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.2826	1301	2401	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	82.0594	1299	2401	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	81.9948	1304	2401	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	81.7259	1192	2401	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.6984	1330	2401	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	81.6015	1226	2401	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	81.4135	992	2401	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.3852	1318	2401	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.3707	1358	2401	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.3626	1120	2401	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	81.2537	1286	2401	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	80.9956	1089	2401	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.9736	1132	2401	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	80.9725	1297	2401	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	80.9587	1100	2401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:06,785] [INFO] DFAST Taxonomy check result was written to GCF_014655855.1_ASM1465585v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:06,785] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:06,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:06,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference/checkm_data
[2024-01-25 18:47:06,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:06,856] [INFO] Task started: CheckM
[2024-01-25 18:47:06,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014655855.1_ASM1465585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014655855.1_ASM1465585v1_genomic.fna/checkm_input GCF_014655855.1_ASM1465585v1_genomic.fna/checkm_result
[2024-01-25 18:48:47,822] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:47,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:47,850] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:47,850] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:47,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014655855.1_ASM1465585v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:47,851] [INFO] Task started: Blastn
[2024-01-25 18:48:47,851] [INFO] Running command: blastn -query GCF_014655855.1_ASM1465585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2546d94a-fd28-4df8-bafc-a0cb0a2f68ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_014655855.1_ASM1465585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:49,874] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:49,877] [INFO] Selected 21 target genomes.
[2024-01-25 18:48:49,877] [INFO] Target genome list was writen to GCF_014655855.1_ASM1465585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:49,908] [INFO] Task started: fastANI
[2024-01-25 18:48:49,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb92987e-4612-4e5c-a5a0-20cecf2337aa/GCF_014655855.1_ASM1465585v1_genomic.fna.gz --refList GCF_014655855.1_ASM1465585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014655855.1_ASM1465585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:27,873] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:27,885] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:27,886] [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_014207445.1	s__Streptomyces candidus	99.9936	2386	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_014650415.1	s__Streptomyces spiroverticillatus	86.1862	1646	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005981925.1	s__Streptomyces albidochromogenes	83.226	1202	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	-
GCF_014650755.1	s__Streptomyces chryseus	82.9586	1346	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	99.26	99.24	0.89	0.85	3	-
GCF_000429085.1	s__Streptomyces flavidovirens	82.8178	1338	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.82	0.82	2	-
GCF_001746415.1	s__Streptomyces agglomeratus	82.7662	1441	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_018614055.1	s__Streptomyces sp018614055	82.5868	1323	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614615.1	s__Streptomyces sp018614615	82.5465	1333	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	82.3607	1135	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	82.3039	1296	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_000725545.1	s__Streptomyces exfoliatus	82.089	1294	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_014596475.1	s__Streptomyces sp014596475	82.039	1247	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	81.9568	1312	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_006539185.1	s__Streptomyces gardneri	81.8961	1323	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCA_004010275.1	s__Streptomyces huasconensis	81.8201	1274	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418325.1	s__Streptomyces atriruber	81.7042	1194	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684775.1	s__Streptomyces sp004684775	81.7007	1182	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556545.1	s__Streptomyces formicae	81.6327	1371	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	81.0313	1241	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045025.1	s__Streptomyces ureilyticus	80.6424	1167	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	80.5368	1149	2401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:27,888] [INFO] GTDB search result was written to GCF_014655855.1_ASM1465585v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:27,888] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:27,892] [INFO] DFAST_QC result json was written to GCF_014655855.1_ASM1465585v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:27,892] [INFO] DFAST_QC completed!
[2024-01-25 18:49:27,893] [INFO] Total running time: 0h3m22s