[2023-03-17 03:50:13,816] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,816] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference
[2023-03-17 03:50:15,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,102] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,102] [INFO] Running command: cat /var/lib/cwl/stg95548f18-79e1-4bf0-ad39-3af07727ef60/OceanDNA-b10261.fa | prodigal -d OceanDNA-b10261/cds.fna -a OceanDNA-b10261/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:25,644] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:25,644] [INFO] Task started: HMMsearch
[2023-03-17 03:50:25,644] [INFO] Running command: hmmsearch --tblout OceanDNA-b10261/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference/reference_markers.hmm OceanDNA-b10261/protein.faa > /dev/null
[2023-03-17 03:50:25,831] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:25,832] [INFO] Found 6/6 markers.
[2023-03-17 03:50:25,844] [INFO] Query marker FASTA was written to OceanDNA-b10261/markers.fasta
[2023-03-17 03:50:25,845] [INFO] Task started: Blastn
[2023-03-17 03:50:25,845] [INFO] Running command: blastn -query OceanDNA-b10261/markers.fasta -db /var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference/reference_markers.fasta -out OceanDNA-b10261/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:26,451] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:26,452] [INFO] Selected 24 target genomes.
[2023-03-17 03:50:26,452] [INFO] Target genome list was writen to OceanDNA-b10261/target_genomes.txt
[2023-03-17 03:50:26,471] [INFO] Task started: fastANI
[2023-03-17 03:50:26,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg95548f18-79e1-4bf0-ad39-3af07727ef60/OceanDNA-b10261.fa --refList OceanDNA-b10261/target_genomes.txt --output OceanDNA-b10261/fastani_result.tsv --threads 1
[2023-03-17 03:50:40,436] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:40,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:40,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:40,449] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:40,449] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:50:40,449] [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 glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	77.2262	146	573	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.2005	145	573	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.1604	160	573	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	77.1566	151	573	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.1538	192	573	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.1117	151	573	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.0995	188	573	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.0956	166	573	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.0133	169	573	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.9839	168	573	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.9683	179	573	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.9593	188	573	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.9472	181	573	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.9396	181	573	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.8276	151	573	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.8006	169	573	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	76.6606	140	573	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.6443	170	573	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.5571	120	573	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.5079	150	573	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.3367	112	573	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.1838	98	573	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:40,450] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10261/tc_result.tsv
[2023-03-17 03:50:40,450] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:40,450] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:40,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference/checkm_data
[2023-03-17 03:50:40,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:40,454] [INFO] Task started: CheckM
[2023-03-17 03:50:40,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10261/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10261/checkm_input OceanDNA-b10261/checkm_result
[2023-03-17 03:51:11,165] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:11,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:11,199] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:11,199] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:11,199] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10261/markers.fasta)
[2023-03-17 03:51:11,199] [INFO] Task started: Blastn
[2023-03-17 03:51:11,199] [INFO] Running command: blastn -query OceanDNA-b10261/markers.fasta -db /var/lib/cwl/stg291f98a9-f8f4-48ea-b3ea-44d6b8c7ce77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10261/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:12,038] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:12,039] [INFO] Selected 16 target genomes.
[2023-03-17 03:51:12,039] [INFO] Target genome list was writen to OceanDNA-b10261/target_genomes_gtdb.txt
[2023-03-17 03:51:12,165] [INFO] Task started: fastANI
[2023-03-17 03:51:12,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg95548f18-79e1-4bf0-ad39-3af07727ef60/OceanDNA-b10261.fa --refList OceanDNA-b10261/target_genomes_gtdb.txt --output OceanDNA-b10261/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:20,728] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:20,738] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:51:20,738] [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_905479435.1	s__SCGC-AAA160-P02 sp905479435	92.3071	382	573	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_015665265.1	s__SCGC-AAA160-P02 sp015665265	85.1429	440	573	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	84.0746	361	573	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_000383355.1	s__SCGC-AAA160-P02 sp000383355	82.5228	434	573	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	77.3408	202	573	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	77.2184	205	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	77.0638	168	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	76.7184	155	573	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	76.6718	179	573	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	76.6443	170	573	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_014062345.1	s__Tenacibaculum pelagium	76.6442	141	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004762155.1	s__Tenacibaculum sp004762155	76.6416	158	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	76.523	108	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.4068	152	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_002813915.1	s__Tenacibaculum sp002813915	76.2719	107	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106565.1	s__Lutibacter oricola	76.2026	97	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:20,738] [INFO] GTDB search result was written to OceanDNA-b10261/result_gtdb.tsv
[2023-03-17 03:51:20,744] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:20,746] [INFO] DFAST_QC result json was written to OceanDNA-b10261/dqc_result.json
[2023-03-17 03:51:20,746] [INFO] DFAST_QC completed!
[2023-03-17 03:51:20,746] [INFO] Total running time: 0h1m7s