[2023-03-15 17:46:31,637] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,639] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference
[2023-03-15 17:46:32,811] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,812] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,812] [INFO] Running command: cat /var/lib/cwl/stgdae466e4-a6d2-41da-819e-ae336094b654/OceanDNA-b10050.fa | prodigal -d OceanDNA-b10050/cds.fna -a OceanDNA-b10050/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:47,319] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:47,319] [INFO] Task started: HMMsearch
[2023-03-15 17:46:47,319] [INFO] Running command: hmmsearch --tblout OceanDNA-b10050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference/reference_markers.hmm OceanDNA-b10050/protein.faa > /dev/null
[2023-03-15 17:46:47,573] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:47,573] [INFO] Found 6/6 markers.
[2023-03-15 17:46:47,598] [INFO] Query marker FASTA was written to OceanDNA-b10050/markers.fasta
[2023-03-15 17:46:47,598] [INFO] Task started: Blastn
[2023-03-15 17:46:47,598] [INFO] Running command: blastn -query OceanDNA-b10050/markers.fasta -db /var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference/reference_markers.fasta -out OceanDNA-b10050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:48,236] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:48,244] [INFO] Selected 18 target genomes.
[2023-03-15 17:46:48,244] [INFO] Target genome list was writen to OceanDNA-b10050/target_genomes.txt
[2023-03-15 17:46:48,256] [INFO] Task started: fastANI
[2023-03-15 17:46:48,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae466e4-a6d2-41da-819e-ae336094b654/OceanDNA-b10050.fa --refList OceanDNA-b10050/target_genomes.txt --output OceanDNA-b10050/fastani_result.tsv --threads 1
[2023-03-15 17:46:58,996] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:58,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:58,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:59,008] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:59,008] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:46:59,008] [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
Polaribacter gangjinensis	strain=JCM 16152	GCA_020532765.1	574710	574710	type	True	82.4541	544	693	95	below_threshold
Polaribacter gangjinensis	strain=KCTC 22729	GCA_002954645.1	574710	574710	type	True	82.4208	537	693	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.5074	374	693	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.4354	384	693	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.4226	336	693	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.2824	299	693	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	78.2378	345	693	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.2343	351	693	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.1845	353	693	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.1842	351	693	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.1508	326	693	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.091	341	693	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.0662	341	693	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.9427	296	693	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.9231	312	693	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	77.8927	328	693	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.8699	324	693	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.6343	306	693	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:46:59,011] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10050/tc_result.tsv
[2023-03-15 17:46:59,016] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:59,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:59,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference/checkm_data
[2023-03-15 17:46:59,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:59,022] [INFO] Task started: CheckM
[2023-03-15 17:46:59,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10050/checkm_input OceanDNA-b10050/checkm_result
[2023-03-15 17:47:39,515] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:39,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:39,521] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:39,522] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:39,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10050/markers.fasta)
[2023-03-15 17:47:39,523] [INFO] Task started: Blastn
[2023-03-15 17:47:39,523] [INFO] Running command: blastn -query OceanDNA-b10050/markers.fasta -db /var/lib/cwl/stg0564f498-6a3c-4cb7-8cb4-d13635ac4b66/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:40,601] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:40,605] [INFO] Selected 11 target genomes.
[2023-03-15 17:47:40,605] [INFO] Target genome list was writen to OceanDNA-b10050/target_genomes_gtdb.txt
[2023-03-15 17:47:40,617] [INFO] Task started: fastANI
[2023-03-15 17:47:40,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae466e4-a6d2-41da-819e-ae336094b654/OceanDNA-b10050.fa --refList OceanDNA-b10050/target_genomes_gtdb.txt --output OceanDNA-b10050/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:48,009] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:48,016] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:47:48,016] [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
GCA_002340765.1	s__Polaribacter sp002340765	99.8243	543	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.32	98.94	0.76	0.72	3	conclusive
GCF_015767435.1	s__Polaribacter sp015767435	87.4833	579	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873065.1	s__Polaribacter sp001873065	85.5829	558	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.94	99.89	0.95	0.94	8	-
GCF_002954645.1	s__Polaribacter gangjinensis	82.4314	536	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	78.4354	384	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105145.1	s__Polaribacter sp900105145	78.3488	361	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943715.1	s__Polaribacter filamentus	78.1962	351	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	78.1845	353	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014784055.1	s__Polaribacter haliotis	78.0656	341	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000981625.1	s__Polaribacter sp000981625	77.8317	256	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	77.6327	308	693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:48,017] [INFO] GTDB search result was written to OceanDNA-b10050/result_gtdb.tsv
[2023-03-15 17:47:48,017] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:48,021] [INFO] DFAST_QC result json was written to OceanDNA-b10050/dqc_result.json
[2023-03-15 17:47:48,021] [INFO] DFAST_QC completed!
[2023-03-15 17:47:48,021] [INFO] Total running time: 0h1m16s