[2023-03-16 22:45:35,371] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:45:35,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:45:35,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference
[2023-03-16 22:45:37,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:45:37,282] [INFO] Task started: Prodigal
[2023-03-16 22:45:37,283] [INFO] Running command: cat /var/lib/cwl/stgc4a19b2c-672c-40d4-9624-509175fd7bb0/OceanDNA-b10298.fa | prodigal -d OceanDNA-b10298/cds.fna -a OceanDNA-b10298/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:45:57,195] [INFO] Task succeeded: Prodigal
[2023-03-16 22:45:57,195] [INFO] Task started: HMMsearch
[2023-03-16 22:45:57,195] [INFO] Running command: hmmsearch --tblout OceanDNA-b10298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference/reference_markers.hmm OceanDNA-b10298/protein.faa > /dev/null
[2023-03-16 22:45:57,389] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:45:57,389] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc4a19b2c-672c-40d4-9624-509175fd7bb0/OceanDNA-b10298.fa]
[2023-03-16 22:45:57,409] [INFO] Query marker FASTA was written to OceanDNA-b10298/markers.fasta
[2023-03-16 22:45:57,411] [INFO] Task started: Blastn
[2023-03-16 22:45:57,411] [INFO] Running command: blastn -query OceanDNA-b10298/markers.fasta -db /var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference/reference_markers.fasta -out OceanDNA-b10298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:45:57,964] [INFO] Task succeeded: Blastn
[2023-03-16 22:45:57,965] [INFO] Selected 24 target genomes.
[2023-03-16 22:45:57,966] [INFO] Target genome list was writen to OceanDNA-b10298/target_genomes.txt
[2023-03-16 22:45:57,977] [INFO] Task started: fastANI
[2023-03-16 22:45:57,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a19b2c-672c-40d4-9624-509175fd7bb0/OceanDNA-b10298.fa --refList OceanDNA-b10298/target_genomes.txt --output OceanDNA-b10298/fastani_result.tsv --threads 1
[2023-03-16 22:46:11,667] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:11,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:46:11,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:46:11,681] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:46:11,682] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 22:46:11,682] [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
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.405	234	1042	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.3408	252	1042	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.2547	289	1042	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.2122	206	1042	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.1844	256	1042	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.1394	230	1042	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.1063	238	1042	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.0854	242	1042	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.037	207	1042	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.006	221	1042	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	76.981	187	1042	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	76.9419	189	1042	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.9374	211	1042	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	76.9142	184	1042	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	76.875	210	1042	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.8638	259	1042	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.8634	170	1042	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.8494	229	1042	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.8311	233	1042	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	76.745	189	1042	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.7344	172	1042	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.6438	223	1042	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	75.9891	125	1042	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	75.9632	124	1042	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 22:46:11,682] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10298/tc_result.tsv
[2023-03-16 22:46:11,682] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:46:11,682] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:46:11,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference/checkm_data
[2023-03-16 22:46:11,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:46:11,687] [INFO] Task started: CheckM
[2023-03-16 22:46:11,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10298/checkm_input OceanDNA-b10298/checkm_result
[2023-03-16 22:47:02,474] [INFO] Task succeeded: CheckM
[2023-03-16 22:47:02,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:47:02,477] [INFO] ===== Completeness check finished =====
[2023-03-16 22:47:02,477] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:47:02,477] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10298/markers.fasta)
[2023-03-16 22:47:02,478] [INFO] Task started: Blastn
[2023-03-16 22:47:02,478] [INFO] Running command: blastn -query OceanDNA-b10298/markers.fasta -db /var/lib/cwl/stg02887585-d74e-4eb1-aa06-7802717abe06/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:47:03,246] [INFO] Task succeeded: Blastn
[2023-03-16 22:47:03,247] [INFO] Selected 27 target genomes.
[2023-03-16 22:47:03,247] [INFO] Target genome list was writen to OceanDNA-b10298/target_genomes_gtdb.txt
[2023-03-16 22:47:03,870] [INFO] Task started: fastANI
[2023-03-16 22:47:03,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a19b2c-672c-40d4-9624-509175fd7bb0/OceanDNA-b10298.fa --refList OceanDNA-b10298/target_genomes_gtdb.txt --output OceanDNA-b10298/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:47:18,717] [INFO] Task succeeded: fastANI
[2023-03-16 22:47:18,732] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 22:47:18,732] [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	78.4742	273	1042	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	78.0735	298	1042	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	-
GCF_000766795.1	s__Polaribacter sp000766795	77.4872	281	1042	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	77.4322	157	1042	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_001889045.1	s__Tenacibaculum_A todarodis	77.4296	232	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	77.4234	267	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	77.4218	224	1042	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_007827455.1	s__VISM01 sp007827455	77.3789	256	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	77.2516	173	1042	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	-
GCF_014352875.1	s__Polaribacter sp014352875	77.2449	290	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	77.2426	269	1042	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	77.1082	236	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	77.0579	211	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	77.019	248	1042	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	77.006	221	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	76.981	187	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	76.9418	189	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	76.926	212	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	76.9021	210	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_008124875.1	s__Tenacibaculum adriaticum	76.875	210	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	76.8719	155	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.858	204	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCA_018663625.1	s__Polaribacter sp018663625	76.7844	170	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_003867015.1	s__Tenacibaculum singaporense	76.7567	188	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.7344	172	1042	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	76.7291	215	1042	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_003384935.1	s__Lutibacter oceani	75.9995	124	1042	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 22:47:18,732] [INFO] GTDB search result was written to OceanDNA-b10298/result_gtdb.tsv
[2023-03-16 22:47:18,732] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:47:18,735] [INFO] DFAST_QC result json was written to OceanDNA-b10298/dqc_result.json
[2023-03-16 22:47:18,735] [INFO] DFAST_QC completed!
[2023-03-16 22:47:18,735] [INFO] Total running time: 0h1m43s