[2023-03-15 09:48:18,526] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:18,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:18,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference
[2023-03-15 09:48:19,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:19,653] [INFO] Task started: Prodigal
[2023-03-15 09:48:19,654] [INFO] Running command: cat /var/lib/cwl/stgf237653d-5b32-49bf-bb42-ebbb6d9a1549/OceanDNA-b6288.fa | prodigal -d OceanDNA-b6288/cds.fna -a OceanDNA-b6288/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:35,519] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:35,520] [INFO] Task started: HMMsearch
[2023-03-15 09:48:35,520] [INFO] Running command: hmmsearch --tblout OceanDNA-b6288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference/reference_markers.hmm OceanDNA-b6288/protein.faa > /dev/null
[2023-03-15 09:48:35,768] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:35,768] [INFO] Found 6/6 markers.
[2023-03-15 09:48:35,783] [INFO] Query marker FASTA was written to OceanDNA-b6288/markers.fasta
[2023-03-15 09:48:35,783] [INFO] Task started: Blastn
[2023-03-15 09:48:35,783] [INFO] Running command: blastn -query OceanDNA-b6288/markers.fasta -db /var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference/reference_markers.fasta -out OceanDNA-b6288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:36,395] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:36,396] [INFO] Selected 21 target genomes.
[2023-03-15 09:48:36,396] [INFO] Target genome list was writen to OceanDNA-b6288/target_genomes.txt
[2023-03-15 09:48:36,400] [INFO] Task started: fastANI
[2023-03-15 09:48:36,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgf237653d-5b32-49bf-bb42-ebbb6d9a1549/OceanDNA-b6288.fa --refList OceanDNA-b6288/target_genomes.txt --output OceanDNA-b6288/fastani_result.tsv --threads 1
[2023-03-15 09:48:48,778] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:48,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:48,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:48,790] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:48,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:48:48,790] [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 pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	78.4349	305	798	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.3767	315	798	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.3382	306	798	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.2352	332	798	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.2233	325	798	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	78.2212	270	798	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	78.2021	248	798	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	78.1212	215	798	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.1132	331	798	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.0925	313	798	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.0495	299	798	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	78.0458	273	798	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.0053	297	798	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	77.8832	241	798	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	77.8545	225	798	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.8022	263	798	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.7931	268	798	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.7728	298	798	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.6485	218	798	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	77.6056	227	798	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	77.5899	224	798	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:48:48,790] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6288/tc_result.tsv
[2023-03-15 09:48:48,790] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:48,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:48,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference/checkm_data
[2023-03-15 09:48:48,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:48,796] [INFO] Task started: CheckM
[2023-03-15 09:48:48,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6288/checkm_input OceanDNA-b6288/checkm_result
[2023-03-15 09:49:30,553] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:30,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:30,555] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:30,556] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:30,556] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6288/markers.fasta)
[2023-03-15 09:49:30,556] [INFO] Task started: Blastn
[2023-03-15 09:49:30,556] [INFO] Running command: blastn -query OceanDNA-b6288/markers.fasta -db /var/lib/cwl/stgc2b67c3c-c0b7-450a-b8a0-dfb0afebf6f4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:31,428] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:31,429] [INFO] Selected 22 target genomes.
[2023-03-15 09:49:31,429] [INFO] Target genome list was writen to OceanDNA-b6288/target_genomes_gtdb.txt
[2023-03-15 09:49:31,700] [INFO] Task started: fastANI
[2023-03-15 09:49:31,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgf237653d-5b32-49bf-bb42-ebbb6d9a1549/OceanDNA-b6288.fa --refList OceanDNA-b6288/target_genomes_gtdb.txt --output OceanDNA-b6288/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:46,278] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:46,290] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:46,290] [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_016763595.1	s__Polaribacter_A sp016763595	80.1576	282	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373385.1	s__Polaribacter_A sp013373385	79.1471	401	798	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_009796785.1	s__Polaribacter sp009796785	78.4973	303	798	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	78.4593	329	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643655.1	s__Polaribacter_A pacificus	78.4481	304	798	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_007827455.1	s__VISM01 sp007827455	78.4036	317	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	78.2433	280	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	78.2282	324	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	78.2269	310	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_014062345.1	s__Tenacibaculum pelagium	78.2021	248	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239505.1	s__Tenacibaculum piscium	78.1792	213	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_003664185.1	s__Tenacibaculum discolor	78.1212	215	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	78.0458	273	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_018861005.1	s__Polaribacter vadi_A	78.0064	316	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	77.9383	234	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	77.8832	241	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	77.8684	260	798	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	77.8628	273	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	77.6485	218	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_900239185.1	s__Tenacibaculum finnmarkense_A	77.6056	227	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	99.00	98.36	0.95	0.91	6	-
GCF_003335085.1	s__Polaribacter sp003335085	77.4822	234	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	77.2291	196	798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:46,291] [INFO] GTDB search result was written to OceanDNA-b6288/result_gtdb.tsv
[2023-03-15 09:49:46,291] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:46,293] [INFO] DFAST_QC result json was written to OceanDNA-b6288/dqc_result.json
[2023-03-15 09:49:46,293] [INFO] DFAST_QC completed!
[2023-03-15 09:49:46,293] [INFO] Total running time: 0h1m28s