[2023-03-16 15:26:08,198] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,198] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,198] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference
[2023-03-16 15:26:09,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:09,503] [INFO] Task started: Prodigal
[2023-03-16 15:26:09,503] [INFO] Running command: cat /var/lib/cwl/stg462603e2-111a-4afb-9294-ae2ec3ed47ef/OceanDNA-b10297.fa | prodigal -d OceanDNA-b10297/cds.fna -a OceanDNA-b10297/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:40,624] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:40,624] [INFO] Task started: HMMsearch
[2023-03-16 15:26:40,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b10297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference/reference_markers.hmm OceanDNA-b10297/protein.faa > /dev/null
[2023-03-16 15:26:40,984] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:40,985] [INFO] Found 6/6 markers.
[2023-03-16 15:26:41,006] [INFO] Query marker FASTA was written to OceanDNA-b10297/markers.fasta
[2023-03-16 15:26:41,014] [INFO] Task started: Blastn
[2023-03-16 15:26:41,014] [INFO] Running command: blastn -query OceanDNA-b10297/markers.fasta -db /var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference/reference_markers.fasta -out OceanDNA-b10297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:41,879] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:41,880] [INFO] Selected 24 target genomes.
[2023-03-16 15:26:41,880] [INFO] Target genome list was writen to OceanDNA-b10297/target_genomes.txt
[2023-03-16 15:26:41,891] [INFO] Task started: fastANI
[2023-03-16 15:26:41,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg462603e2-111a-4afb-9294-ae2ec3ed47ef/OceanDNA-b10297.fa --refList OceanDNA-b10297/target_genomes.txt --output OceanDNA-b10297/fastani_result.tsv --threads 1
[2023-03-16 15:26:57,968] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:57,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:57,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:57,980] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:57,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:26:57,981] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.9589	297	1075	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.7785	274	1075	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.7648	281	1075	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.7495	287	1075	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.7413	266	1075	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.7364	304	1075	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.7315	222	1075	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.6964	305	1075	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.6807	253	1075	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.6755	305	1075	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.6403	268	1075	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.61	278	1075	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.563	260	1075	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	77.5625	227	1075	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	77.5609	239	1075	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.5485	287	1075	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.4779	298	1075	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	77.4713	206	1075	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.4687	258	1075	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.4309	255	1075	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	77.2223	213	1075	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	76.1888	66	1075	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	75.9292	50	1075	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:26:57,981] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10297/tc_result.tsv
[2023-03-16 15:26:57,981] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:57,981] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:57,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference/checkm_data
[2023-03-16 15:26:57,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:58,385] [INFO] Task started: CheckM
[2023-03-16 15:26:58,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10297/checkm_input OceanDNA-b10297/checkm_result
[2023-03-16 15:28:00,772] [INFO] Task succeeded: CheckM
[2023-03-16 15:28:00,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:28:00,775] [INFO] ===== Completeness check finished =====
[2023-03-16 15:28:00,775] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:28:00,776] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10297/markers.fasta)
[2023-03-16 15:28:00,776] [INFO] Task started: Blastn
[2023-03-16 15:28:00,776] [INFO] Running command: blastn -query OceanDNA-b10297/markers.fasta -db /var/lib/cwl/stg7a5bbbbc-b884-4e25-9b6e-5a9a60360b3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:28:01,674] [INFO] Task succeeded: Blastn
[2023-03-16 15:28:01,675] [INFO] Selected 22 target genomes.
[2023-03-16 15:28:01,675] [INFO] Target genome list was writen to OceanDNA-b10297/target_genomes_gtdb.txt
[2023-03-16 15:28:02,237] [INFO] Task started: fastANI
[2023-03-16 15:28:02,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg462603e2-111a-4afb-9294-ae2ec3ed47ef/OceanDNA-b10297.fa --refList OceanDNA-b10297/target_genomes_gtdb.txt --output OceanDNA-b10297/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:28:23,343] [INFO] Task succeeded: fastANI
[2023-03-16 15:28:23,355] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:28:23,355] [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_016763215.1	s__SCGC-AAA160-P02 sp016763215	78.9184	306	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	78.6226	332	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	78.2667	266	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCF_000766795.1	s__Polaribacter sp000766795	77.9839	315	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	77.9365	189	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	77.8046	305	1075	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	77.7475	303	1075	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	77.7268	317	1075	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	77.6694	289	1075	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	77.6363	263	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	77.5897	322	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	77.5758	183	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	77.5633	211	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	77.4795	280	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	77.4713	206	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCA_018663625.1	s__Polaribacter sp018663625	77.4659	187	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.4459	260	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_003867075.1	s__Tenacibaculum mesophilum	77.4366	212	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	77.4283	201	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCA_004762155.1	s__Tenacibaculum sp004762155	77.3877	258	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373385.1	s__Polaribacter_A sp013373385	77.3825	222	1075	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_002836595.1	s__Tenacibaculum sp002836595	77.3149	269	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:28:23,356] [INFO] GTDB search result was written to OceanDNA-b10297/result_gtdb.tsv
[2023-03-16 15:28:23,356] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:28:23,358] [INFO] DFAST_QC result json was written to OceanDNA-b10297/dqc_result.json
[2023-03-16 15:28:23,358] [INFO] DFAST_QC completed!
[2023-03-16 15:28:23,358] [INFO] Total running time: 0h2m15s