[2023-03-18 20:40:39,439] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference
[2023-03-18 20:40:41,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,208] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,208] [INFO] Running command: cat /var/lib/cwl/stg14861d60-a5c9-466f-83b2-700fc8e9b6ad/OceanDNA-b9950.fa | prodigal -d OceanDNA-b9950/cds.fna -a OceanDNA-b9950/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:50,186] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:50,186] [INFO] Task started: HMMsearch
[2023-03-18 20:40:50,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b9950/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference/reference_markers.hmm OceanDNA-b9950/protein.faa > /dev/null
[2023-03-18 20:40:50,438] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:50,438] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg14861d60-a5c9-466f-83b2-700fc8e9b6ad/OceanDNA-b9950.fa]
[2023-03-18 20:40:50,452] [INFO] Query marker FASTA was written to OceanDNA-b9950/markers.fasta
[2023-03-18 20:40:50,452] [INFO] Task started: Blastn
[2023-03-18 20:40:50,452] [INFO] Running command: blastn -query OceanDNA-b9950/markers.fasta -db /var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference/reference_markers.fasta -out OceanDNA-b9950/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:51,067] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:51,068] [INFO] Selected 16 target genomes.
[2023-03-18 20:40:51,068] [INFO] Target genome list was writen to OceanDNA-b9950/target_genomes.txt
[2023-03-18 20:40:51,072] [INFO] Task started: fastANI
[2023-03-18 20:40:51,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg14861d60-a5c9-466f-83b2-700fc8e9b6ad/OceanDNA-b9950.fa --refList OceanDNA-b9950/target_genomes.txt --output OceanDNA-b9950/fastani_result.tsv --threads 1
[2023-03-18 20:41:00,983] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:00,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:00,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:00,994] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:00,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:00,994] [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 atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.3044	295	444	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.3003	321	444	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.2653	311	444	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.191	316	444	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.9789	297	444	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	79.9032	305	444	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.7863	290	444	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	79.6571	303	444	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	79.51	285	444	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.4903	283	444	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.4746	283	444	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.4483	278	444	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	79.4481	289	444	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.9379	265	444	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.8778	218	444	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	75.9544	58	444	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:00,994] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9950/tc_result.tsv
[2023-03-18 20:41:00,994] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:00,994] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:00,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference/checkm_data
[2023-03-18 20:41:00,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:00,999] [INFO] Task started: CheckM
[2023-03-18 20:41:00,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9950/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9950/checkm_input OceanDNA-b9950/checkm_result
[2023-03-18 20:41:28,113] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:28,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:28,115] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:28,115] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:28,116] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9950/markers.fasta)
[2023-03-18 20:41:28,116] [INFO] Task started: Blastn
[2023-03-18 20:41:28,116] [INFO] Running command: blastn -query OceanDNA-b9950/markers.fasta -db /var/lib/cwl/stg7f3d6017-b8db-4a26-9e81-1c0340322dc4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9950/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:29,114] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:29,115] [INFO] Selected 14 target genomes.
[2023-03-18 20:41:29,115] [INFO] Target genome list was writen to OceanDNA-b9950/target_genomes_gtdb.txt
[2023-03-18 20:41:29,142] [INFO] Task started: fastANI
[2023-03-18 20:41:29,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg14861d60-a5c9-466f-83b2-700fc8e9b6ad/OceanDNA-b9950.fa --refList OceanDNA-b9950/target_genomes_gtdb.txt --output OceanDNA-b9950/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:37,782] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:37,790] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:41:37,790] [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_905181765.1	s__Polaribacter sp905181765	94.4587	327	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_002831685.1	s__Polaribacter sp002831685	82.1802	345	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	81.9678	347	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	80.6476	251	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	80.3586	319	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	80.3044	295	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	80.2745	312	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	80.2189	325	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_009796785.1	s__Polaribacter sp009796785	80.1843	308	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	79.8852	306	444	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	79.7698	300	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	79.7695	308	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_007997085.1	s__Polaribacter sp007997085	79.0511	281	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:37,791] [INFO] GTDB search result was written to OceanDNA-b9950/result_gtdb.tsv
[2023-03-18 20:41:37,791] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:37,792] [INFO] DFAST_QC result json was written to OceanDNA-b9950/dqc_result.json
[2023-03-18 20:41:37,792] [INFO] DFAST_QC completed!
[2023-03-18 20:41:37,793] [INFO] Total running time: 0h0m58s