[2024-01-24 11:12:26,275] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:26,280] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:26,280] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference
[2024-01-24 11:12:27,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,613] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c228af8-be1b-41c3-8775-8eebb27cab5c/GCF_014489635.1_ASM1448963v1_genomic.fna.gz | prodigal -d GCF_014489635.1_ASM1448963v1_genomic.fna/cds.fna -a GCF_014489635.1_ASM1448963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:59,617] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:59,617] [INFO] Task started: HMMsearch
[2024-01-24 11:12:59,618] [INFO] Running command: hmmsearch --tblout GCF_014489635.1_ASM1448963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference/reference_markers.hmm GCF_014489635.1_ASM1448963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:00,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:00,052] [INFO] Found 6/6 markers.
[2024-01-24 11:13:00,132] [INFO] Query marker FASTA was written to GCF_014489635.1_ASM1448963v1_genomic.fna/markers.fasta
[2024-01-24 11:13:00,133] [INFO] Task started: Blastn
[2024-01-24 11:13:00,133] [INFO] Running command: blastn -query GCF_014489635.1_ASM1448963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference/reference_markers.fasta -out GCF_014489635.1_ASM1448963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:01,485] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:01,490] [INFO] Selected 29 target genomes.
[2024-01-24 11:13:01,490] [INFO] Target genome list was writen to GCF_014489635.1_ASM1448963v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:01,500] [INFO] Task started: fastANI
[2024-01-24 11:13:01,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c228af8-be1b-41c3-8775-8eebb27cab5c/GCF_014489635.1_ASM1448963v1_genomic.fna.gz --refList GCF_014489635.1_ASM1448963v1_genomic.fna/target_genomes.txt --output GCF_014489635.1_ASM1448963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:09,574] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:09,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:09,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:09,598] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:09,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:09,598] [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 roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	100.0	3312	3315	95	conclusive
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	83.6715	1901	3315	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	83.6501	1588	3315	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	83.61	1901	3315	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	83.5445	1648	3315	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	83.505	1644	3315	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.37	1924	3315	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	83.3627	1701	3315	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	83.2801	1817	3315	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	83.274	1691	3315	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	83.264	1807	3315	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.2488	1673	3315	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	83.2019	1774	3315	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	83.1527	1791	3315	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	83.0032	1380	3315	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	82.9078	1532	3315	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	82.9036	1820	3315	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	82.8929	1576	3315	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	82.7903	1855	3315	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	82.7452	1632	3315	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	82.7383	1651	3315	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	82.6835	1697	3315	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	82.6767	1656	3315	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	82.6506	1605	3315	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	82.6421	1651	3315	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	82.6126	1620	3315	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	82.5878	1641	3315	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	82.4068	1844	3315	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	82.2774	1689	3315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:09,600] [INFO] DFAST Taxonomy check result was written to GCF_014489635.1_ASM1448963v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:09,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:09,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:09,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference/checkm_data
[2024-01-24 11:14:09,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:09,688] [INFO] Task started: CheckM
[2024-01-24 11:14:09,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489635.1_ASM1448963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489635.1_ASM1448963v1_genomic.fna/checkm_input GCF_014489635.1_ASM1448963v1_genomic.fna/checkm_result
[2024-01-24 11:17:20,407] [INFO] Task succeeded: CheckM
[2024-01-24 11:17:20,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:17:20,439] [INFO] ===== Completeness check finished =====
[2024-01-24 11:17:20,439] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:17:20,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489635.1_ASM1448963v1_genomic.fna/markers.fasta)
[2024-01-24 11:17:20,440] [INFO] Task started: Blastn
[2024-01-24 11:17:20,440] [INFO] Running command: blastn -query GCF_014489635.1_ASM1448963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0756047-2585-4e53-9dfd-6e26d3903fec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489635.1_ASM1448963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:17:22,509] [INFO] Task succeeded: Blastn
[2024-01-24 11:17:22,514] [INFO] Selected 17 target genomes.
[2024-01-24 11:17:22,514] [INFO] Target genome list was writen to GCF_014489635.1_ASM1448963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:17:22,530] [INFO] Task started: fastANI
[2024-01-24 11:17:22,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c228af8-be1b-41c3-8775-8eebb27cab5c/GCF_014489635.1_ASM1448963v1_genomic.fna.gz --refList GCF_014489635.1_ASM1448963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489635.1_ASM1448963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:18:01,363] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:01,380] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:18:01,381] [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_014489635.1	s__Streptomyces sp014489635	100.0	3313	3315	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_001419795.1	s__Streptomyces niveiscabiei	89.2454	1825	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	99.33	0.94	0.94	2	-
GCF_000242715.1	s__Streptomyces acidiscabies	88.7748	2479	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.11	97.67	0.95	0.89	7	-
GCA_002027195.1	s__Streptomyces sp002027195	83.6864	1617	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_001514205.1	s__Streptomyces griseoruber	83.6669	1902	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	83.5722	1643	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_014648915.1	s__Streptomyces phaeofaciens	83.5614	1912	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	83.5274	1916	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001184025.1	s__Streptomyces sp001184025	83.4761	1757	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	98.49	0.84	0.84	2	-
GCF_003143935.1	s__Streptomyces sp003143935	83.364	1837	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514125.1	s__Streptomyces longwoodensis	83.3277	1707	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_001514195.1	s__Streptomyces griseorubiginosus	83.2927	1815	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.34	95.64	0.90	0.86	7	-
GCF_002920535.1	s__Streptomyces sp002920535	83.1515	1588	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	82.9487	1480	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091315.1	s__Streptomyces sp900091315	82.892	1672	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715615.1	s__Streptomyces cinnabarinus	82.8555	1699	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	82.5014	1749	3315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:18:01,383] [INFO] GTDB search result was written to GCF_014489635.1_ASM1448963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:18:01,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:18:01,389] [INFO] DFAST_QC result json was written to GCF_014489635.1_ASM1448963v1_genomic.fna/dqc_result.json
[2024-01-24 11:18:01,389] [INFO] DFAST_QC completed!
[2024-01-24 11:18:01,389] [INFO] Total running time: 0h5m35s