[2024-01-24 14:47:08,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference
[2024-01-24 14:47:09,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,752] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cec6807-dd77-44bc-b347-9f41a14d7188/GCF_014207445.1_ASM1420744v1_genomic.fna.gz | prodigal -d GCF_014207445.1_ASM1420744v1_genomic.fna/cds.fna -a GCF_014207445.1_ASM1420744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:31,293] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:31,293] [INFO] Task started: HMMsearch
[2024-01-24 14:47:31,294] [INFO] Running command: hmmsearch --tblout GCF_014207445.1_ASM1420744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference/reference_markers.hmm GCF_014207445.1_ASM1420744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:31,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:31,719] [INFO] Found 6/6 markers.
[2024-01-24 14:47:31,777] [INFO] Query marker FASTA was written to GCF_014207445.1_ASM1420744v1_genomic.fna/markers.fasta
[2024-01-24 14:47:31,778] [INFO] Task started: Blastn
[2024-01-24 14:47:31,778] [INFO] Running command: blastn -query GCF_014207445.1_ASM1420744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference/reference_markers.fasta -out GCF_014207445.1_ASM1420744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:33,093] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:33,100] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:33,100] [INFO] Target genome list was writen to GCF_014207445.1_ASM1420744v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:33,116] [INFO] Task started: fastANI
[2024-01-24 14:47:33,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cec6807-dd77-44bc-b347-9f41a14d7188/GCF_014207445.1_ASM1420744v1_genomic.fna.gz --refList GCF_014207445.1_ASM1420744v1_genomic.fna/target_genomes.txt --output GCF_014207445.1_ASM1420744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:14,690] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:14,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:14,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:14,708] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:48:14,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:14,709] [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=DSM 40141	GCA_014207445.1	67283	67283	type	True	100.0	2433	2436	95	conclusive
Streptomyces candidus	strain=JCM 4629	GCA_014655855.1	67283	67283	type	True	99.9908	2379	2436	95	conclusive
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	86.2839	1627	2436	95	below_threshold
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	83.275	1075	2436	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	83.2514	1207	2436	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	82.9022	1364	2436	95	below_threshold
Streptomyces flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	82.8198	1333	2436	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	82.2899	1098	2436	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.252	1310	2436	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	82.0287	1304	2436	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	81.9307	1316	2436	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	81.6837	1200	2436	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.5868	1347	2436	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	81.4917	1243	2436	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.4912	1350	2436	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	81.4464	971	2436	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.3965	1314	2436	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.388	1140	2436	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	81.24	1297	2436	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.0631	1292	2436	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	81.0061	1106	2436	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.9418	1138	2436	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	80.9011	1107	2436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:14,710] [INFO] DFAST Taxonomy check result was written to GCF_014207445.1_ASM1420744v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:14,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:14,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:14,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference/checkm_data
[2024-01-24 14:48:14,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:14,786] [INFO] Task started: CheckM
[2024-01-24 14:48:14,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207445.1_ASM1420744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207445.1_ASM1420744v1_genomic.fna/checkm_input GCF_014207445.1_ASM1420744v1_genomic.fna/checkm_result
[2024-01-24 14:49:58,405] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:58,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:58,437] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:58,438] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:58,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207445.1_ASM1420744v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:58,439] [INFO] Task started: Blastn
[2024-01-24 14:49:58,439] [INFO] Running command: blastn -query GCF_014207445.1_ASM1420744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg698dce4c-6eba-40f5-8c1e-1cb84c85c9af/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207445.1_ASM1420744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:00,725] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:00,729] [INFO] Selected 21 target genomes.
[2024-01-24 14:50:00,729] [INFO] Target genome list was writen to GCF_014207445.1_ASM1420744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:00,746] [INFO] Task started: fastANI
[2024-01-24 14:50:00,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cec6807-dd77-44bc-b347-9f41a14d7188/GCF_014207445.1_ASM1420744v1_genomic.fna.gz --refList GCF_014207445.1_ASM1420744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207445.1_ASM1420744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:40,980] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:41,004] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:41,004] [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	100.0	2433	2436	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	86.2161	1637	2436	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	83.2662	1204	2436	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	82.9204	1359	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	99.26	99.24	0.89	0.85	3	-
GCF_001746415.1	s__Streptomyces agglomeratus	82.8252	1418	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_000429085.1	s__Streptomyces flavidovirens	82.8143	1334	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.82	0.82	2	-
GCF_018614055.1	s__Streptomyces sp018614055	82.6475	1311	2436	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	82.5093	1334	2436	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	82.4895	1126	2436	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	82.2526	1308	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_014596475.1	s__Streptomyces sp014596475	82.0694	1243	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725545.1	s__Streptomyces exfoliatus	82.0354	1303	2436	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	81.9254	1312	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	81.9184	1326	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCA_004010275.1	s__Streptomyces huasconensis	81.8954	1285	2436	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	81.6851	1371	2436	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	81.6725	1193	2436	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	81.6656	1202	2436	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	80.9405	1279	2436	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	80.6879	1171	2436	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	80.588	1163	2436	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 14:50:41,013] [INFO] GTDB search result was written to GCF_014207445.1_ASM1420744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:41,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:41,019] [INFO] DFAST_QC result json was written to GCF_014207445.1_ASM1420744v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:41,019] [INFO] DFAST_QC completed!
[2024-01-24 14:50:41,019] [INFO] Total running time: 0h3m33s