[2023-03-18 23:40:00,501] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,501] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,501] [INFO] DQC Reference Directory: /var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference
[2023-03-18 23:40:01,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,590] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,590] [INFO] Running command: cat /var/lib/cwl/stg317e57d8-fb15-48e4-97b8-13720716e9e5/OceanDNA-b9907.fa | prodigal -d OceanDNA-b9907/cds.fna -a OceanDNA-b9907/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:14,994] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:14,994] [INFO] Task started: HMMsearch
[2023-03-18 23:40:14,994] [INFO] Running command: hmmsearch --tblout OceanDNA-b9907/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference/reference_markers.hmm OceanDNA-b9907/protein.faa > /dev/null
[2023-03-18 23:40:15,180] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:15,181] [INFO] Found 6/6 markers.
[2023-03-18 23:40:15,195] [INFO] Query marker FASTA was written to OceanDNA-b9907/markers.fasta
[2023-03-18 23:40:15,197] [INFO] Task started: Blastn
[2023-03-18 23:40:15,197] [INFO] Running command: blastn -query OceanDNA-b9907/markers.fasta -db /var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference/reference_markers.fasta -out OceanDNA-b9907/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:15,767] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:15,767] [INFO] Selected 20 target genomes.
[2023-03-18 23:40:15,767] [INFO] Target genome list was writen to OceanDNA-b9907/target_genomes.txt
[2023-03-18 23:40:15,780] [INFO] Task started: fastANI
[2023-03-18 23:40:15,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg317e57d8-fb15-48e4-97b8-13720716e9e5/OceanDNA-b9907.fa --refList OceanDNA-b9907/target_genomes.txt --output OceanDNA-b9907/fastani_result.tsv --threads 1
[2023-03-18 23:40:27,541] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:27,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:27,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:27,553] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:27,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:40:27,553] [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 butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	79.3004	393	688	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.9811	352	688	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.9571	354	688	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.8027	364	688	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.7971	362	688	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.6492	356	688	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.5917	345	688	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.5542	342	688	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.4548	314	688	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.4391	329	688	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.4037	342	688	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.3155	346	688	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.265	283	688	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.2558	323	688	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.0918	298	688	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.0044	247	688	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	77.9709	336	688	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.6702	254	688	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	77.6673	251	688	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.3725	180	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:40:27,553] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9907/tc_result.tsv
[2023-03-18 23:40:27,554] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:27,554] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:27,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference/checkm_data
[2023-03-18 23:40:27,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:27,558] [INFO] Task started: CheckM
[2023-03-18 23:40:27,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9907/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9907/checkm_input OceanDNA-b9907/checkm_result
[2023-03-18 23:41:04,467] [INFO] Task succeeded: CheckM
[2023-03-18 23:41:04,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.71%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:41:04,470] [INFO] ===== Completeness check finished =====
[2023-03-18 23:41:04,470] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:41:04,470] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9907/markers.fasta)
[2023-03-18 23:41:04,471] [INFO] Task started: Blastn
[2023-03-18 23:41:04,472] [INFO] Running command: blastn -query OceanDNA-b9907/markers.fasta -db /var/lib/cwl/stgf196f7c5-eb23-4a9d-a78e-0841646ba0a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9907/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:41:05,266] [INFO] Task succeeded: Blastn
[2023-03-18 23:41:05,267] [INFO] Selected 19 target genomes.
[2023-03-18 23:41:05,267] [INFO] Target genome list was writen to OceanDNA-b9907/target_genomes_gtdb.txt
[2023-03-18 23:41:05,290] [INFO] Task started: fastANI
[2023-03-18 23:41:05,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg317e57d8-fb15-48e4-97b8-13720716e9e5/OceanDNA-b9907.fa --refList OceanDNA-b9907/target_genomes_gtdb.txt --output OceanDNA-b9907/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:16,974] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:16,985] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:41:16,985] [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_018608545.1	s__Polaribacter sp018608545	85.3104	537	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	-
GCF_000766795.1	s__Polaribacter sp000766795	79.7375	425	688	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	79.2947	394	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	79.1998	390	688	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	78.997	370	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_001640115.1	s__Polaribacter atrinae	78.9571	354	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	78.809	364	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	78.7852	363	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002163835.1	s__Polaribacter sp002163835	78.6846	394	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	78.637	357	688	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	78.5555	322	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	78.5491	343	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005885675.1	s__Polaribacter aestuariivivens	78.5324	349	688	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	78.4485	294	688	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	78.3268	345	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017569185.1	s__Polaribacter sp017569185	78.26	322	688	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	77.9815	335	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201235.1	s__Polaribacter tangerinus	77.633	251	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.374	180	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:16,985] [INFO] GTDB search result was written to OceanDNA-b9907/result_gtdb.tsv
[2023-03-18 23:41:16,985] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:16,987] [INFO] DFAST_QC result json was written to OceanDNA-b9907/dqc_result.json
[2023-03-18 23:41:16,987] [INFO] DFAST_QC completed!
[2023-03-18 23:41:16,987] [INFO] Total running time: 0h1m16s