[2024-01-24 14:30:47,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,130] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference
[2024-01-24 14:30:48,441] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,442] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,442] [INFO] Running command: gunzip -c /var/lib/cwl/stgd24621aa-f343-4164-a40c-821933ca1732/GCF_007483685.1_ASM748368v1_genomic.fna.gz | prodigal -d GCF_007483685.1_ASM748368v1_genomic.fna/cds.fna -a GCF_007483685.1_ASM748368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:11,131] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:11,131] [INFO] Task started: HMMsearch
[2024-01-24 14:31:11,131] [INFO] Running command: hmmsearch --tblout GCF_007483685.1_ASM748368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference/reference_markers.hmm GCF_007483685.1_ASM748368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:11,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:11,455] [INFO] Found 6/6 markers.
[2024-01-24 14:31:11,518] [INFO] Query marker FASTA was written to GCF_007483685.1_ASM748368v1_genomic.fna/markers.fasta
[2024-01-24 14:31:11,519] [INFO] Task started: Blastn
[2024-01-24 14:31:11,519] [INFO] Running command: blastn -query GCF_007483685.1_ASM748368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference/reference_markers.fasta -out GCF_007483685.1_ASM748368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:12,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:12,253] [INFO] Selected 24 target genomes.
[2024-01-24 14:31:12,254] [INFO] Target genome list was writen to GCF_007483685.1_ASM748368v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:12,264] [INFO] Task started: fastANI
[2024-01-24 14:31:12,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgd24621aa-f343-4164-a40c-821933ca1732/GCF_007483685.1_ASM748368v1_genomic.fna.gz --refList GCF_007483685.1_ASM748368v1_genomic.fna/target_genomes.txt --output GCF_007483685.1_ASM748368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:32,173] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:32,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:32,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:32,189] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:32,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:32,190] [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
Litoribacter populi	strain=XAAS-A1	GCA_007483685.1	2598460	2598460	type	True	100.0	1498	1499	95	conclusive
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	78.0924	125	1499	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	77.8619	112	1499	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	77.8109	120	1499	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	77.6092	127	1499	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	77.1407	95	1499	95	below_threshold
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	76.9013	72	1499	95	below_threshold
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	76.8427	84	1499	95	below_threshold
Algoriphagus marinus	strain=am2	GCA_001936475.1	1925762	1925762	type	True	76.8275	65	1499	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	76.7283	74	1499	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	76.691	86	1499	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.6731	90	1499	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.6507	108	1499	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	76.3611	58	1499	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	76.3538	112	1499	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.2545	76	1499	95	below_threshold
Rhodonellum psychrophilum	strain=GCM71	GCA_000473765.1	336828	336828	type	True	76.1986	104	1499	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	76.1893	75	1499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:32,191] [INFO] DFAST Taxonomy check result was written to GCF_007483685.1_ASM748368v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:32,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:32,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:32,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference/checkm_data
[2024-01-24 14:31:32,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:32,239] [INFO] Task started: CheckM
[2024-01-24 14:31:32,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007483685.1_ASM748368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007483685.1_ASM748368v1_genomic.fna/checkm_input GCF_007483685.1_ASM748368v1_genomic.fna/checkm_result
[2024-01-24 14:32:38,354] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:38,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:38,377] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:38,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:38,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007483685.1_ASM748368v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:38,379] [INFO] Task started: Blastn
[2024-01-24 14:32:38,379] [INFO] Running command: blastn -query GCF_007483685.1_ASM748368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4087ae2-1907-4e0f-9028-e70d5a864911/dqc_reference/reference_markers_gtdb.fasta -out GCF_007483685.1_ASM748368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:39,214] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:39,217] [INFO] Selected 20 target genomes.
[2024-01-24 14:32:39,218] [INFO] Target genome list was writen to GCF_007483685.1_ASM748368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:39,232] [INFO] Task started: fastANI
[2024-01-24 14:32:39,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgd24621aa-f343-4164-a40c-821933ca1732/GCF_007483685.1_ASM748368v1_genomic.fna.gz --refList GCF_007483685.1_ASM748368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007483685.1_ASM748368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:55,754] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:55,770] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:55,770] [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_007483685.1	s__Litoribacter sp007483685	100.0	1498	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018500185.1	s__Litoribacter ruber	82.3879	895	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_015533855.1	s__Echinicola sp015533855	78.2262	125	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000714815.1	s__Anditalea andensis	78.051	180	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Anditalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	77.8619	112	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	77.8304	66	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	77.8109	120	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	77.1407	95	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.914	114	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	76.9013	72	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129785.1	s__Algoriphagus halophilus	76.8427	84	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.7712	93	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	76.691	86	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.4392	123	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.348	111	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.2777	75	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565295.1	s__Negadavirga sp003565295	76.1761	60	1499	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:55,772] [INFO] GTDB search result was written to GCF_007483685.1_ASM748368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:55,773] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:55,779] [INFO] DFAST_QC result json was written to GCF_007483685.1_ASM748368v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:55,779] [INFO] DFAST_QC completed!
[2024-01-24 14:32:55,779] [INFO] Total running time: 0h2m9s