[2024-01-24 12:40:35,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference
[2024-01-24 12:40:36,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,633] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg63936452-02d3-40c6-94bb-8c3c2a11557f/GCF_003194085.1_ASM319408v1_genomic.fna.gz | prodigal -d GCF_003194085.1_ASM319408v1_genomic.fna/cds.fna -a GCF_003194085.1_ASM319408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:42,139] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:42,140] [INFO] Task started: HMMsearch
[2024-01-24 12:40:42,140] [INFO] Running command: hmmsearch --tblout GCF_003194085.1_ASM319408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference/reference_markers.hmm GCF_003194085.1_ASM319408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:42,363] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:42,365] [INFO] Found 6/6 markers.
[2024-01-24 12:40:42,389] [INFO] Query marker FASTA was written to GCF_003194085.1_ASM319408v1_genomic.fna/markers.fasta
[2024-01-24 12:40:42,390] [INFO] Task started: Blastn
[2024-01-24 12:40:42,390] [INFO] Running command: blastn -query GCF_003194085.1_ASM319408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference/reference_markers.fasta -out GCF_003194085.1_ASM319408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:43,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:43,174] [INFO] Selected 20 target genomes.
[2024-01-24 12:40:43,175] [INFO] Target genome list was writen to GCF_003194085.1_ASM319408v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:43,187] [INFO] Task started: fastANI
[2024-01-24 12:40:43,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg63936452-02d3-40c6-94bb-8c3c2a11557f/GCF_003194085.1_ASM319408v1_genomic.fna.gz --refList GCF_003194085.1_ASM319408v1_genomic.fna/target_genomes.txt --output GCF_003194085.1_ASM319408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:54,299] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:54,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:54,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:54,318] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:54,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:54,318] [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
Aurantimicrobium photophilum	strain=MWH-Mo1	GCA_003194085.1	1987356	1987356	type	True	100.0	582	582	95	conclusive
Aurantimicrobium minutum	strain=KNC	GCA_002355535.1	708131	708131	type	True	82.4723	316	582	95	below_threshold
Alpinimonas psychrophila	strain=DSM 23737	GCA_014137865.1	748908	748908	type	True	78.1417	123	582	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	77.954	82	582	95	below_threshold
Mycetocola saprophilus	strain=NRRL B-24119	GCA_000718085.1	76636	76636	type	True	77.8796	79	582	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	77.7714	59	582	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	77.5974	65	582	95	below_threshold
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	77.5782	82	582	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	77.5009	72	582	95	below_threshold
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	77.3529	80	582	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_004134805.1	592376	592376	type	True	77.2527	64	582	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	77.251	76	582	95	below_threshold
Mycetocola zhadangensis	strain=ZD1-4	GCA_003668565.1	1164595	1164595	type	True	76.9715	82	582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,320] [INFO] DFAST Taxonomy check result was written to GCF_003194085.1_ASM319408v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:54,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:54,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:54,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference/checkm_data
[2024-01-24 12:40:54,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:54,347] [INFO] Task started: CheckM
[2024-01-24 12:40:54,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003194085.1_ASM319408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003194085.1_ASM319408v1_genomic.fna/checkm_input GCF_003194085.1_ASM319408v1_genomic.fna/checkm_result
[2024-01-24 12:41:17,294] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:17,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:17,311] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:17,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:17,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003194085.1_ASM319408v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:17,313] [INFO] Task started: Blastn
[2024-01-24 12:41:17,313] [INFO] Running command: blastn -query GCF_003194085.1_ASM319408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c3bc25e-e351-4375-8d15-0e04d26fd538/dqc_reference/reference_markers_gtdb.fasta -out GCF_003194085.1_ASM319408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:18,405] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:18,409] [INFO] Selected 16 target genomes.
[2024-01-24 12:41:18,410] [INFO] Target genome list was writen to GCF_003194085.1_ASM319408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:18,429] [INFO] Task started: fastANI
[2024-01-24 12:41:18,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg63936452-02d3-40c6-94bb-8c3c2a11557f/GCF_003194085.1_ASM319408v1_genomic.fna.gz --refList GCF_003194085.1_ASM319408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003194085.1_ASM319408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:25,115] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:25,130] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:25,130] [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_003194085.1	s__Aurantimicrobium sp003194085	100.0	582	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002355535.1	s__Aurantimicrobium minutum	82.4723	316	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325955.1	s__Aurantimicrobium sp003325955	81.9987	323	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aurantimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137865.1	s__Alpinimonas psychrophila	78.1417	123	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Alpinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859205.1	s__CAIOLM01 sp903859205	78.1005	108	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__CAIOLM01	95.0	99.95	99.95	0.98	0.98	2	-
GCF_001423185.1	s__Plantibacter sp001423185	77.7448	59	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Plantibacter	95.0	98.46	98.46	0.97	0.97	3	-
GCA_009704705.1	s__RFQD01 sp009704705	77.5325	67	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__RFQD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856975.1	s__Plantibacter cousiniae	77.4334	71	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Plantibacter	95.9127	96.92	96.01	0.91	0.89	11	-
GCF_002797685.1	s__Rhodoglobus amurskyensis	77.3529	80	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015864945.1	s__Rhodoglobus sp015864945	77.3483	77	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402485.1	s__Cryobacterium sp004402485	77.2665	65	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107435.1	s__Herbiconiux ginsengi	77.251	76	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002024505.1	s__Plantibacter flavus_A	77.2487	71	582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Plantibacter	95.1912	97.90	97.77	0.92	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:25,132] [INFO] GTDB search result was written to GCF_003194085.1_ASM319408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:25,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:25,136] [INFO] DFAST_QC result json was written to GCF_003194085.1_ASM319408v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:25,136] [INFO] DFAST_QC completed!
[2024-01-24 12:41:25,136] [INFO] Total running time: 0h0m50s