[2023-03-16 17:20:08,862] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:20:08,862] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:20:08,862] [INFO] DQC Reference Directory: /var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference
[2023-03-16 17:20:10,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:20:10,657] [INFO] Task started: Prodigal
[2023-03-16 17:20:10,658] [INFO] Running command: cat /var/lib/cwl/stg08f62444-a3ca-4a8f-8fa6-ac7dd7aaec2a/OceanDNA-b6287.fa | prodigal -d OceanDNA-b6287/cds.fna -a OceanDNA-b6287/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:20:24,719] [INFO] Task succeeded: Prodigal
[2023-03-16 17:20:24,719] [INFO] Task started: HMMsearch
[2023-03-16 17:20:24,719] [INFO] Running command: hmmsearch --tblout OceanDNA-b6287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference/reference_markers.hmm OceanDNA-b6287/protein.faa > /dev/null
[2023-03-16 17:20:24,990] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:20:24,991] [INFO] Found 6/6 markers.
[2023-03-16 17:20:25,016] [INFO] Query marker FASTA was written to OceanDNA-b6287/markers.fasta
[2023-03-16 17:20:25,018] [INFO] Task started: Blastn
[2023-03-16 17:20:25,018] [INFO] Running command: blastn -query OceanDNA-b6287/markers.fasta -db /var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference/reference_markers.fasta -out OceanDNA-b6287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:20:25,807] [INFO] Task succeeded: Blastn
[2023-03-16 17:20:25,807] [INFO] Selected 28 target genomes.
[2023-03-16 17:20:25,808] [INFO] Target genome list was writen to OceanDNA-b6287/target_genomes.txt
[2023-03-16 17:20:25,822] [INFO] Task started: fastANI
[2023-03-16 17:20:25,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg08f62444-a3ca-4a8f-8fa6-ac7dd7aaec2a/OceanDNA-b6287.fa --refList OceanDNA-b6287/target_genomes.txt --output OceanDNA-b6287/fastani_result.tsv --threads 1
[2023-03-16 17:20:45,720] [INFO] Task succeeded: fastANI
[2023-03-16 17:20:45,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:20:45,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:20:45,739] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:20:45,739] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:20:45,739] [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	78.3557	271	675	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.3515	269	675	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.2922	274	675	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	78.2616	279	675	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.1915	305	675	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.1781	284	675	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.1677	290	675	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.1645	289	675	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.1196	266	675	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.9986	266	675	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.961	263	675	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.9236	285	675	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.9158	282	675	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.908	261	675	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.808	216	675	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.7479	276	675	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.7004	220	675	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.6584	220	675	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.6186	223	675	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	77.6146	176	675	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.3756	214	675	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	77.3702	173	675	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	77.3527	174	675	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.3254	250	675	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.2493	184	675	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.2489	252	675	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	77.0928	184	675	95	below_threshold
Tenacibaculum maritimum		GCA_900119795.1	107401	107401	type	True	76.8351	161	675	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:20:45,739] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6287/tc_result.tsv
[2023-03-16 17:20:45,739] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:20:45,739] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:20:45,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference/checkm_data
[2023-03-16 17:20:45,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:20:45,761] [INFO] Task started: CheckM
[2023-03-16 17:20:45,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6287/checkm_input OceanDNA-b6287/checkm_result
[2023-03-16 17:21:23,534] [INFO] Task succeeded: CheckM
[2023-03-16 17:21:23,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:21:23,536] [INFO] ===== Completeness check finished =====
[2023-03-16 17:21:23,537] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:21:23,537] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6287/markers.fasta)
[2023-03-16 17:21:23,538] [INFO] Task started: Blastn
[2023-03-16 17:21:23,538] [INFO] Running command: blastn -query OceanDNA-b6287/markers.fasta -db /var/lib/cwl/stg139e66eb-93e9-4fd4-a98f-1a9800952993/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:21:24,387] [INFO] Task succeeded: Blastn
[2023-03-16 17:21:24,388] [INFO] Selected 23 target genomes.
[2023-03-16 17:21:24,388] [INFO] Target genome list was writen to OceanDNA-b6287/target_genomes_gtdb.txt
[2023-03-16 17:21:24,400] [INFO] Task started: fastANI
[2023-03-16 17:21:24,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg08f62444-a3ca-4a8f-8fa6-ac7dd7aaec2a/OceanDNA-b6287.fa --refList OceanDNA-b6287/target_genomes_gtdb.txt --output OceanDNA-b6287/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:21:38,266] [INFO] Task succeeded: fastANI
[2023-03-16 17:21:38,279] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:21:38,279] [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	79.4223	234	675	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	78.7491	348	675	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_002163835.1	s__Polaribacter sp002163835	78.5618	302	675	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	78.5348	301	675	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	78.3716	285	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643655.1	s__Polaribacter_A pacificus	78.3502	272	675	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_002163675.1	s__Polaribacter sp002163675	78.3058	296	675	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	78.1916	283	675	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_018861005.1	s__Polaribacter vadi_A	78.1394	283	675	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	78.1249	265	675	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	77.961	263	675	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	77.9325	280	675	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	77.9088	261	675	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	77.8545	282	675	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	77.8115	258	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	77.7522	214	675	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	77.7479	276	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	77.694	232	675	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	77.4671	217	675	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	77.3769	226	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.3621	215	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_002954685.1	s__Polaribacter porphyrae	77.2274	254	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	77.1131	209	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:21:38,279] [INFO] GTDB search result was written to OceanDNA-b6287/result_gtdb.tsv
[2023-03-16 17:21:38,279] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:21:38,282] [INFO] DFAST_QC result json was written to OceanDNA-b6287/dqc_result.json
[2023-03-16 17:21:38,282] [INFO] DFAST_QC completed!
[2023-03-16 17:21:38,282] [INFO] Total running time: 0h1m29s