[2023-03-18 03:27:00,945] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference
[2023-03-18 03:27:02,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,640] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,640] [INFO] Running command: cat /var/lib/cwl/stg97d1758f-9a70-4409-bba5-04df24d51f20/OceanDNA-b10108.fa | prodigal -d OceanDNA-b10108/cds.fna -a OceanDNA-b10108/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:17,321] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:17,321] [INFO] Task started: HMMsearch
[2023-03-18 03:27:17,321] [INFO] Running command: hmmsearch --tblout OceanDNA-b10108/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference/reference_markers.hmm OceanDNA-b10108/protein.faa > /dev/null
[2023-03-18 03:27:17,501] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:17,502] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg97d1758f-9a70-4409-bba5-04df24d51f20/OceanDNA-b10108.fa]
[2023-03-18 03:27:17,517] [INFO] Query marker FASTA was written to OceanDNA-b10108/markers.fasta
[2023-03-18 03:27:17,518] [INFO] Task started: Blastn
[2023-03-18 03:27:17,518] [INFO] Running command: blastn -query OceanDNA-b10108/markers.fasta -db /var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference/reference_markers.fasta -out OceanDNA-b10108/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:18,116] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:18,116] [INFO] Selected 17 target genomes.
[2023-03-18 03:27:18,117] [INFO] Target genome list was writen to OceanDNA-b10108/target_genomes.txt
[2023-03-18 03:27:18,124] [INFO] Task started: fastANI
[2023-03-18 03:27:18,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d1758f-9a70-4409-bba5-04df24d51f20/OceanDNA-b10108.fa --refList OceanDNA-b10108/target_genomes.txt --output OceanDNA-b10108/fastani_result.tsv --threads 1
[2023-03-18 03:27:27,832] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:27,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:27,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:27,842] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:27,843] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:27,843] [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	78.2321	313	794	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.1327	288	794	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.0828	296	794	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.9983	259	794	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.951	295	794	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.948	284	794	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.9415	292	794	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	77.9094	300	794	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.8469	280	794	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.7204	289	794	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	77.6831	184	794	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.6562	285	794	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.6148	281	794	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.5002	271	794	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.4985	253	794	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	77.3057	238	794	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.2789	258	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:27,843] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10108/tc_result.tsv
[2023-03-18 03:27:27,843] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:27,843] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:27,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference/checkm_data
[2023-03-18 03:27:27,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:27,848] [INFO] Task started: CheckM
[2023-03-18 03:27:27,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10108/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10108/checkm_input OceanDNA-b10108/checkm_result
[2023-03-18 03:28:07,352] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:07,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:07,354] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:07,354] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:07,354] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10108/markers.fasta)
[2023-03-18 03:28:07,355] [INFO] Task started: Blastn
[2023-03-18 03:28:07,355] [INFO] Running command: blastn -query OceanDNA-b10108/markers.fasta -db /var/lib/cwl/stg10967c8f-cf73-4733-8cc2-7080616f1563/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10108/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:08,191] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:08,192] [INFO] Selected 21 target genomes.
[2023-03-18 03:28:08,192] [INFO] Target genome list was writen to OceanDNA-b10108/target_genomes_gtdb.txt
[2023-03-18 03:28:08,209] [INFO] Task started: fastANI
[2023-03-18 03:28:08,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d1758f-9a70-4409-bba5-04df24d51f20/OceanDNA-b10108.fa --refList OceanDNA-b10108/target_genomes_gtdb.txt --output OceanDNA-b10108/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:20,647] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:20,659] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:28:20,659] [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_000383355.1	s__SCGC-AAA160-P02 sp000383355	80.3359	395	794	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	79.0361	309	794	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	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	78.6736	238	794	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_016763215.1	s__SCGC-AAA160-P02 sp016763215	78.4864	239	794	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_000766795.1	s__Polaribacter sp000766795	78.4259	325	794	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	78.4099	328	794	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	78.2569	316	794	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	78.1436	280	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	77.9679	282	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	77.9623	294	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	77.953	283	794	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_016858305.2	s__Polaribacter sp016858305	77.8796	272	794	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	77.8756	291	794	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	77.8237	282	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	77.7204	289	794	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	77.6347	287	794	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	77.6003	288	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_002836595.1	s__Tenacibaculum sp002836595	77.3788	257	794	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	77.3774	293	794	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	77.3755	193	794	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	77.3057	238	794	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:28:20,659] [INFO] GTDB search result was written to OceanDNA-b10108/result_gtdb.tsv
[2023-03-18 03:28:20,659] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:20,661] [INFO] DFAST_QC result json was written to OceanDNA-b10108/dqc_result.json
[2023-03-18 03:28:20,661] [INFO] DFAST_QC completed!
[2023-03-18 03:28:20,661] [INFO] Total running time: 0h1m20s