[2024-01-24 13:37:25,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,946] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference
[2024-01-24 13:37:27,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,175] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg46a0bc23-e1cd-49c7-92d5-d4aa2c04dde0/GCF_009193215.1_ASM919321v1_genomic.fna.gz | prodigal -d GCF_009193215.1_ASM919321v1_genomic.fna/cds.fna -a GCF_009193215.1_ASM919321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:37,286] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:37,286] [INFO] Task started: HMMsearch
[2024-01-24 13:37:37,286] [INFO] Running command: hmmsearch --tblout GCF_009193215.1_ASM919321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference/reference_markers.hmm GCF_009193215.1_ASM919321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:37,552] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:37,553] [INFO] Found 6/6 markers.
[2024-01-24 13:37:37,592] [INFO] Query marker FASTA was written to GCF_009193215.1_ASM919321v1_genomic.fna/markers.fasta
[2024-01-24 13:37:37,592] [INFO] Task started: Blastn
[2024-01-24 13:37:37,593] [INFO] Running command: blastn -query GCF_009193215.1_ASM919321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference/reference_markers.fasta -out GCF_009193215.1_ASM919321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:38,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:38,234] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:38,235] [INFO] Target genome list was writen to GCF_009193215.1_ASM919321v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:38,241] [INFO] Task started: fastANI
[2024-01-24 13:37:38,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a0bc23-e1cd-49c7-92d5-d4aa2c04dde0/GCF_009193215.1_ASM919321v1_genomic.fna.gz --refList GCF_009193215.1_ASM919321v1_genomic.fna/target_genomes.txt --output GCF_009193215.1_ASM919321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:49,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:49,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:49,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:49,908] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:49,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:49,908] [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
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	100.0	1045	1047	95	conclusive
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	78.9019	339	1047	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	77.8881	180	1047	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	77.6695	181	1047	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	77.5707	102	1047	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	77.4838	193	1047	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.2484	141	1047	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.2005	149	1047	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.1982	155	1047	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.1571	136	1047	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.1324	140	1047	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.0434	155	1047	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.9187	121	1047	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	76.8737	128	1047	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	76.8608	126	1047	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.8213	116	1047	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.8042	168	1047	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.6425	172	1047	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	76.6132	130	1047	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.5564	90	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:49,910] [INFO] DFAST Taxonomy check result was written to GCF_009193215.1_ASM919321v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:49,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:49,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:49,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference/checkm_data
[2024-01-24 13:37:49,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:49,945] [INFO] Task started: CheckM
[2024-01-24 13:37:49,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193215.1_ASM919321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193215.1_ASM919321v1_genomic.fna/checkm_input GCF_009193215.1_ASM919321v1_genomic.fna/checkm_result
[2024-01-24 13:38:21,981] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:21,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:21,996] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:21,996] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:21,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193215.1_ASM919321v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:21,997] [INFO] Task started: Blastn
[2024-01-24 13:38:21,997] [INFO] Running command: blastn -query GCF_009193215.1_ASM919321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc28008e-e0db-4135-9690-0e795430c4eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193215.1_ASM919321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:22,832] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:22,835] [INFO] Selected 17 target genomes.
[2024-01-24 13:38:22,835] [INFO] Target genome list was writen to GCF_009193215.1_ASM919321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:22,856] [INFO] Task started: fastANI
[2024-01-24 13:38:22,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a0bc23-e1cd-49c7-92d5-d4aa2c04dde0/GCF_009193215.1_ASM919321v1_genomic.fna.gz --refList GCF_009193215.1_ASM919321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009193215.1_ASM919321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:32,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:32,500] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:32,500] [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_009193215.1	s__Flavicella marina	100.0	1046	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006381105.1	s__Flavicella sediminum	78.8714	340	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479475.1	s__Flavicella sp905479475	78.179	168	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	77.8675	181	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	77.6732	180	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477565.1	s__Flavicella sp002477565	77.6048	102	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	98.32	98.32	0.91	0.91	2	-
GCF_014643655.1	s__Polaribacter_A pacificus	77.5686	102	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	77.4825	193	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	77.247	142	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	77.1522	138	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105985.1	s__Tenacibaculum sp900105985	77.0162	128	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_900105145.1	s__Polaribacter sp900105145	77.0003	168	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	76.9528	175	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900198195.1	s__Tenacibaculum jejuense	76.9187	121	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	76.8858	140	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001975665.1	s__Polaribacter reichenbachii	76.8092	168	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_018054895.1	s__Lutibacter sp018054895	76.4276	117	1047	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:32,503] [INFO] GTDB search result was written to GCF_009193215.1_ASM919321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:32,504] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:32,507] [INFO] DFAST_QC result json was written to GCF_009193215.1_ASM919321v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:32,507] [INFO] DFAST_QC completed!
[2024-01-24 13:38:32,507] [INFO] Total running time: 0h1m7s