[2024-01-24 10:57:13,195] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,196] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,197] [INFO] DQC Reference Directory: /var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference
[2024-01-24 10:57:14,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,669] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fc5d9ab-235d-4fa8-9054-4001fe3a0f02/GCF_018500185.1_ASM1850018v1_genomic.fna.gz | prodigal -d GCF_018500185.1_ASM1850018v1_genomic.fna/cds.fna -a GCF_018500185.1_ASM1850018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,441] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,441] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,441] [INFO] Running command: hmmsearch --tblout GCF_018500185.1_ASM1850018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference/reference_markers.hmm GCF_018500185.1_ASM1850018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,881] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,944] [INFO] Query marker FASTA was written to GCF_018500185.1_ASM1850018v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,944] [INFO] Task started: Blastn
[2024-01-24 10:57:36,944] [INFO] Running command: blastn -query GCF_018500185.1_ASM1850018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference/reference_markers.fasta -out GCF_018500185.1_ASM1850018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:37,660] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:37,665] [INFO] Selected 18 target genomes.
[2024-01-24 10:57:37,666] [INFO] Target genome list was writen to GCF_018500185.1_ASM1850018v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:37,674] [INFO] Task started: fastANI
[2024-01-24 10:57:37,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc5d9ab-235d-4fa8-9054-4001fe3a0f02/GCF_018500185.1_ASM1850018v1_genomic.fna.gz --refList GCF_018500185.1_ASM1850018v1_genomic.fna/target_genomes.txt --output GCF_018500185.1_ASM1850018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:52,721] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:52,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:52,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:52,733] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:52,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:52,733] [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	82.4656	889	1345	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	77.8436	113	1345	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	77.8072	117	1345	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	77.7275	115	1345	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	77.3505	130	1345	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	77.1295	113	1345	95	below_threshold
Echinicola pacifica	strain=DSM 19836	GCA_000373245.1	346377	346377	type	True	77.1281	109	1345	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.9582	84	1345	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.9236	96	1345	95	below_threshold
Algoriphagus resistens	strain=NH1	GCA_001442615.1	1750590	1750590	type	True	76.8545	84	1345	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.7307	86	1345	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.4632	75	1345	95	below_threshold
Pararhodonellum marinum	strain=SW124	GCA_015354735.1	2755358	2755358	type	True	76.3961	111	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:52,736] [INFO] DFAST Taxonomy check result was written to GCF_018500185.1_ASM1850018v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:52,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:52,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:52,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference/checkm_data
[2024-01-24 10:57:52,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:52,782] [INFO] Task started: CheckM
[2024-01-24 10:57:52,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018500185.1_ASM1850018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018500185.1_ASM1850018v1_genomic.fna/checkm_input GCF_018500185.1_ASM1850018v1_genomic.fna/checkm_result
[2024-01-24 10:58:54,829] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:54,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,849] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:54,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:54,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018500185.1_ASM1850018v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:54,850] [INFO] Task started: Blastn
[2024-01-24 10:58:54,850] [INFO] Running command: blastn -query GCF_018500185.1_ASM1850018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge70a298a-3448-4149-a645-9e062661dc7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018500185.1_ASM1850018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:55,629] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:55,632] [INFO] Selected 21 target genomes.
[2024-01-24 10:58:55,632] [INFO] Target genome list was writen to GCF_018500185.1_ASM1850018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:55,647] [INFO] Task started: fastANI
[2024-01-24 10:58:55,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc5d9ab-235d-4fa8-9054-4001fe3a0f02/GCF_018500185.1_ASM1850018v1_genomic.fna.gz --refList GCF_018500185.1_ASM1850018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018500185.1_ASM1850018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:11,470] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:11,487] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:11,488] [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_018500185.1	s__Litoribacter ruber	100.0	1343	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	conclusive
GCF_007483685.1	s__Litoribacter sp007483685	82.4687	889	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015533855.1	s__Echinicola sp015533855	77.9519	118	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	77.8709	112	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841125.1	s__Echinicola sp014841125	77.8333	116	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	77.7831	113	1345	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	77.4863	186	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Anditalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373245.1	s__Echinicola pacifica	77.1498	108	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007655305.1	s__Algoriphagus sp007655305	76.9844	83	1345	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	76.9236	96	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	76.8209	74	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	76.7535	85	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.4859	74	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.4281	93	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	76.1609	62	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.1483	109	1345	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:11,490] [INFO] GTDB search result was written to GCF_018500185.1_ASM1850018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:11,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:11,494] [INFO] DFAST_QC result json was written to GCF_018500185.1_ASM1850018v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:11,494] [INFO] DFAST_QC completed!
[2024-01-24 10:59:11,494] [INFO] Total running time: 0h1m58s