[2023-03-15 22:10:43,680] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:10:43,680] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:10:43,680] [INFO] DQC Reference Directory: /var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference
[2023-03-15 22:10:44,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:10:44,799] [INFO] Task started: Prodigal
[2023-03-15 22:10:44,799] [INFO] Running command: cat /var/lib/cwl/stgd0478295-adc0-4e80-8381-baf8b0f1d9f2/OceanDNA-b6270.fa | prodigal -d OceanDNA-b6270/cds.fna -a OceanDNA-b6270/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:10:58,996] [INFO] Task succeeded: Prodigal
[2023-03-15 22:10:58,996] [INFO] Task started: HMMsearch
[2023-03-15 22:10:58,996] [INFO] Running command: hmmsearch --tblout OceanDNA-b6270/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference/reference_markers.hmm OceanDNA-b6270/protein.faa > /dev/null
[2023-03-15 22:10:59,192] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:10:59,193] [INFO] Found 6/6 markers.
[2023-03-15 22:10:59,207] [INFO] Query marker FASTA was written to OceanDNA-b6270/markers.fasta
[2023-03-15 22:10:59,209] [INFO] Task started: Blastn
[2023-03-15 22:10:59,209] [INFO] Running command: blastn -query OceanDNA-b6270/markers.fasta -db /var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference/reference_markers.fasta -out OceanDNA-b6270/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:10:59,802] [INFO] Task succeeded: Blastn
[2023-03-15 22:10:59,803] [INFO] Selected 24 target genomes.
[2023-03-15 22:10:59,804] [INFO] Target genome list was writen to OceanDNA-b6270/target_genomes.txt
[2023-03-15 22:10:59,817] [INFO] Task started: fastANI
[2023-03-15 22:10:59,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0478295-adc0-4e80-8381-baf8b0f1d9f2/OceanDNA-b6270.fa --refList OceanDNA-b6270/target_genomes.txt --output OceanDNA-b6270/fastani_result.tsv --threads 1
[2023-03-15 22:11:13,925] [INFO] Task succeeded: fastANI
[2023-03-15 22:11:13,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:11:13,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:11:13,939] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:11:13,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:11:13,940] [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	79.163	414	753	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.1016	363	753	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.8838	411	753	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.8688	416	753	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	78.8548	364	753	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.8452	343	753	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.839	372	753	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.7281	369	753	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	78.6997	363	753	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.6802	370	753	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.6465	369	753	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	78.6426	368	753	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	78.6139	376	753	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.6138	363	753	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.5765	363	753	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.5151	355	753	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.4918	351	753	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.4488	349	753	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.3614	343	753	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	78.1225	318	753	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.0784	322	753	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	78.0395	327	753	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	77.6827	227	753	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	77.5095	258	753	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:11:13,940] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6270/tc_result.tsv
[2023-03-15 22:11:13,940] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:11:13,940] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:11:13,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference/checkm_data
[2023-03-15 22:11:13,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:11:13,944] [INFO] Task started: CheckM
[2023-03-15 22:11:13,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6270/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6270/checkm_input OceanDNA-b6270/checkm_result
[2023-03-15 22:11:51,849] [INFO] Task succeeded: CheckM
[2023-03-15 22:11:51,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:11:51,852] [INFO] ===== Completeness check finished =====
[2023-03-15 22:11:51,852] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:11:51,852] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6270/markers.fasta)
[2023-03-15 22:11:51,853] [INFO] Task started: Blastn
[2023-03-15 22:11:51,853] [INFO] Running command: blastn -query OceanDNA-b6270/markers.fasta -db /var/lib/cwl/stge03799c7-a2a2-42fd-8e86-b5035cea4df9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6270/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:11:52,690] [INFO] Task succeeded: Blastn
[2023-03-15 22:11:52,692] [INFO] Selected 23 target genomes.
[2023-03-15 22:11:52,692] [INFO] Target genome list was writen to OceanDNA-b6270/target_genomes_gtdb.txt
[2023-03-15 22:11:53,001] [INFO] Task started: fastANI
[2023-03-15 22:11:53,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0478295-adc0-4e80-8381-baf8b0f1d9f2/OceanDNA-b6270.fa --refList OceanDNA-b6270/target_genomes_gtdb.txt --output OceanDNA-b6270/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:12:07,175] [INFO] Task succeeded: fastANI
[2023-03-15 22:12:07,188] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:12:07,188] [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	79.5867	266	753	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	79.3013	430	753	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_014352875.1	s__Polaribacter sp014352875	79.145	415	753	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	79.1264	401	753	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	79.1165	397	753	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	79.105	408	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	78.9387	419	753	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	78.8683	416	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014643655.1	s__Polaribacter_A pacificus	78.8548	364	753	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	78.7478	372	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	78.7194	388	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954665.1	s__Polaribacter glomeratus	78.6802	370	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002831685.1	s__Polaribacter sp002831685	78.6778	378	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	78.5834	380	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_002005425.1	s__Polaribacter sp002005425	78.4849	379	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_002943715.1	s__Polaribacter filamentus	78.4808	352	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	78.4721	347	753	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	78.4216	287	753	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	78.3731	342	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	78.296	350	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	78.0187	329	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003335085.1	s__Polaribacter sp003335085	77.7705	311	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867075.1	s__Tenacibaculum mesophilum	77.6732	228	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
--------------------------------------------------------------------------------
[2023-03-15 22:12:07,189] [INFO] GTDB search result was written to OceanDNA-b6270/result_gtdb.tsv
[2023-03-15 22:12:07,189] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:12:07,192] [INFO] DFAST_QC result json was written to OceanDNA-b6270/dqc_result.json
[2023-03-15 22:12:07,192] [INFO] DFAST_QC completed!
[2023-03-15 22:12:07,192] [INFO] Total running time: 0h1m24s