[2024-01-25 17:46:06,140] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:06,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:06,141] [INFO] DQC Reference Directory: /var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference
[2024-01-25 17:46:07,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:07,249] [INFO] Task started: Prodigal
[2024-01-25 17:46:07,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg4abeabad-d9ef-430e-b5cb-556cd75826b7/GCF_014650515.1_ASM1465051v1_genomic.fna.gz | prodigal -d GCF_014650515.1_ASM1465051v1_genomic.fna/cds.fna -a GCF_014650515.1_ASM1465051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:44,417] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:44,417] [INFO] Task started: HMMsearch
[2024-01-25 17:46:44,417] [INFO] Running command: hmmsearch --tblout GCF_014650515.1_ASM1465051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference/reference_markers.hmm GCF_014650515.1_ASM1465051v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:44,738] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:44,739] [INFO] Found 6/6 markers.
[2024-01-25 17:46:44,805] [INFO] Query marker FASTA was written to GCF_014650515.1_ASM1465051v1_genomic.fna/markers.fasta
[2024-01-25 17:46:44,805] [INFO] Task started: Blastn
[2024-01-25 17:46:44,806] [INFO] Running command: blastn -query GCF_014650515.1_ASM1465051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference/reference_markers.fasta -out GCF_014650515.1_ASM1465051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:46,012] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:46,014] [INFO] Selected 21 target genomes.
[2024-01-25 17:46:46,015] [INFO] Target genome list was writen to GCF_014650515.1_ASM1465051v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:46,025] [INFO] Task started: fastANI
[2024-01-25 17:46:46,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg4abeabad-d9ef-430e-b5cb-556cd75826b7/GCF_014650515.1_ASM1465051v1_genomic.fna.gz --refList GCF_014650515.1_ASM1465051v1_genomic.fna/target_genomes.txt --output GCF_014650515.1_ASM1465051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:29,576] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:29,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:29,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:29,589] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:29,589] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:29,589] [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 finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	100.0	3128	3130	95	conclusive
Streptomyces candidus	strain=JCM 4629	GCA_014655855.1	67283	67283	type	True	86.1051	1665	3130	95	below_threshold
Streptomyces candidus	strain=DSM 40141	GCA_014207445.1	67283	67283	type	True	86.0456	1673	3130	95	below_threshold
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	83.5174	1108	3130	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	83.2449	1276	3130	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	83.0397	1475	3130	95	below_threshold
Streptomyces flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	82.9996	1372	3130	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	82.5131	1488	3130	95	below_threshold
Streptomyces violascens	strain=JCM 4424	GCA_014649955.1	67381	67381	type	True	82.4557	1477	3130	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	82.3884	1561	3130	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	82.2555	1400	3130	95	below_threshold
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	82.2455	1410	3130	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.227	1504	3130	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	82.0653	1379	3130	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	81.7623	1545	3130	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.6252	1369	3130	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.4472	1557	3130	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	81.3977	1446	3130	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	81.1372	1432	3130	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	81.074	1393	3130	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	80.9614	1464	3130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:29,591] [INFO] DFAST Taxonomy check result was written to GCF_014650515.1_ASM1465051v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:29,591] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:29,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:29,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference/checkm_data
[2024-01-25 17:47:29,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:29,674] [INFO] Task started: CheckM
[2024-01-25 17:47:29,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650515.1_ASM1465051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650515.1_ASM1465051v1_genomic.fna/checkm_input GCF_014650515.1_ASM1465051v1_genomic.fna/checkm_result
[2024-01-25 17:50:23,221] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:23,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:23,256] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:23,257] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:23,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650515.1_ASM1465051v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:23,258] [INFO] Task started: Blastn
[2024-01-25 17:50:23,258] [INFO] Running command: blastn -query GCF_014650515.1_ASM1465051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09be881a-1ab0-4b13-b398-d59c86b2ae80/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650515.1_ASM1465051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:25,388] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:25,391] [INFO] Selected 19 target genomes.
[2024-01-25 17:50:25,392] [INFO] Target genome list was writen to GCF_014650515.1_ASM1465051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:25,416] [INFO] Task started: fastANI
[2024-01-25 17:50:25,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg4abeabad-d9ef-430e-b5cb-556cd75826b7/GCF_014650515.1_ASM1465051v1_genomic.fna.gz --refList GCF_014650515.1_ASM1465051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650515.1_ASM1465051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:05,495] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:05,506] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:05,506] [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
GCA_014650415.1	s__Streptomyces spiroverticillatus	99.9945	3119	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014207445.1	s__Streptomyces candidus	86.0383	1675	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005981925.1	s__Streptomyces albidochromogenes	83.2155	1280	3130	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	83.0302	1477	3130	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	83.0043	1371	3130	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	82.7404	1516	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_018614615.1	s__Streptomyces sp018614615	82.586	1451	3130	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	82.523	1295	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649955.1	s__Streptomyces violascens	82.5147	1465	3130	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	82.4434	1550	3130	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	82.369	1407	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353505.1	s__Streptomyces sp004353505	82.3403	1421	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_014649715.1	s__Streptomyces lateritius	82.2504	1410	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.94	0.94	2	-
GCF_002382885.1	s__Streptomyces sp002382885	82.2107	1362	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717655.1	s__Streptomyces katrae_B	81.6107	1379	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.60	96.50	0.86	0.86	4	-
GCF_002080455.1	s__Streptomyces sp002080455	81.6032	1409	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_900100315.1	s__Streptomyces indicus	81.4719	1490	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	81.0972	1308	3130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	81.065	1396	3130	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 17:51:05,508] [INFO] GTDB search result was written to GCF_014650515.1_ASM1465051v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:05,509] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:05,512] [INFO] DFAST_QC result json was written to GCF_014650515.1_ASM1465051v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:05,513] [INFO] DFAST_QC completed!
[2024-01-25 17:51:05,513] [INFO] Total running time: 0h4m59s