[2024-01-24 12:45:10,804] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,817] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference
[2024-01-24 12:45:13,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,105] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d4c394b-ad71-4a4f-b456-d0e0925fda95/GCF_016863075.1_ASM1686307v1_genomic.fna.gz | prodigal -d GCF_016863075.1_ASM1686307v1_genomic.fna/cds.fna -a GCF_016863075.1_ASM1686307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:31,290] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:31,290] [INFO] Task started: HMMsearch
[2024-01-24 12:45:31,290] [INFO] Running command: hmmsearch --tblout GCF_016863075.1_ASM1686307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference/reference_markers.hmm GCF_016863075.1_ASM1686307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:31,638] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:31,640] [INFO] Found 6/6 markers.
[2024-01-24 12:45:31,701] [INFO] Query marker FASTA was written to GCF_016863075.1_ASM1686307v1_genomic.fna/markers.fasta
[2024-01-24 12:45:31,701] [INFO] Task started: Blastn
[2024-01-24 12:45:31,701] [INFO] Running command: blastn -query GCF_016863075.1_ASM1686307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference/reference_markers.fasta -out GCF_016863075.1_ASM1686307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:33,106] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:33,109] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:33,110] [INFO] Target genome list was writen to GCF_016863075.1_ASM1686307v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:33,118] [INFO] Task started: fastANI
[2024-01-24 12:45:33,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d4c394b-ad71-4a4f-b456-d0e0925fda95/GCF_016863075.1_ASM1686307v1_genomic.fna.gz --refList GCF_016863075.1_ASM1686307v1_genomic.fna/target_genomes.txt --output GCF_016863075.1_ASM1686307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:00,802] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:00,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:00,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:00,817] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:46:00,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:00,817] [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
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	100.0	2205	2210	95	conclusive
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	99.9972	2202	2210	95	conclusive
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	90.7431	1771	2210	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	90.6927	1795	2210	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	90.5653	1779	2210	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	90.2938	1773	2210	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	90.2541	1744	2210	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	87.0133	1578	2210	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	86.9684	1603	2210	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	82.784	1301	2210	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.4762	1088	2210	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	80.2225	1146	2210	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.0882	1158	2210	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.9401	810	2210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:00,820] [INFO] DFAST Taxonomy check result was written to GCF_016863075.1_ASM1686307v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:00,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:00,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:00,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference/checkm_data
[2024-01-24 12:46:00,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:00,901] [INFO] Task started: CheckM
[2024-01-24 12:46:00,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863075.1_ASM1686307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863075.1_ASM1686307v1_genomic.fna/checkm_input GCF_016863075.1_ASM1686307v1_genomic.fna/checkm_result
[2024-01-24 12:46:58,465] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:58,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:58,535] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:58,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:58,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863075.1_ASM1686307v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:58,537] [INFO] Task started: Blastn
[2024-01-24 12:46:58,537] [INFO] Running command: blastn -query GCF_016863075.1_ASM1686307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b872318-302a-41f3-b69a-6743890aad08/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863075.1_ASM1686307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:00,700] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:00,704] [INFO] Selected 10 target genomes.
[2024-01-24 12:47:00,704] [INFO] Target genome list was writen to GCF_016863075.1_ASM1686307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:00,715] [INFO] Task started: fastANI
[2024-01-24 12:47:00,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d4c394b-ad71-4a4f-b456-d0e0925fda95/GCF_016863075.1_ASM1686307v1_genomic.fna.gz --refList GCF_016863075.1_ASM1686307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863075.1_ASM1686307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:21,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:21,171] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:21,171] [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_014647835.1	s__Microbispora aerata	99.9972	2202	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016863095.1	s__Microbispora siamensis	90.7613	1769	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006334915.2	s__Microbispora catharanthi	90.598	1775	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_014161445.1	s__Microbispora sp014161445	90.3636	1793	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_006874475.1	s__Microbispora hainanensis	90.3231	1769	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_900156315.1	s__Microbispora rosea	90.2033	1777	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_006874465.1	s__Microbispora bryophytorum	90.0124	1699	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_012999535.1	s__Microbispora sp012999535	89.1166	1669	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863015.1	s__Microbispora amethystogenes	87.0116	1578	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_001570365.1	s__Microtetraspora fusca	81.4892	1244	2210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:21,173] [INFO] GTDB search result was written to GCF_016863075.1_ASM1686307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:21,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:21,177] [INFO] DFAST_QC result json was written to GCF_016863075.1_ASM1686307v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:21,177] [INFO] DFAST_QC completed!
[2024-01-24 12:47:21,178] [INFO] Total running time: 0h2m10s