[2023-03-18 10:41:19,237] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:41:19,238] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:41:19,238] [INFO] DQC Reference Directory: /var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference
[2023-03-18 10:41:20,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:41:20,435] [INFO] Task started: Prodigal
[2023-03-18 10:41:20,435] [INFO] Running command: cat /var/lib/cwl/stg46888ce3-dcc6-42af-a682-65395152ed93/OceanDNA-b6819.fa | prodigal -d OceanDNA-b6819/cds.fna -a OceanDNA-b6819/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:41:33,868] [INFO] Task succeeded: Prodigal
[2023-03-18 10:41:33,868] [INFO] Task started: HMMsearch
[2023-03-18 10:41:33,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b6819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference/reference_markers.hmm OceanDNA-b6819/protein.faa > /dev/null
[2023-03-18 10:41:34,027] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:41:34,027] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg46888ce3-dcc6-42af-a682-65395152ed93/OceanDNA-b6819.fa]
[2023-03-18 10:41:34,042] [INFO] Query marker FASTA was written to OceanDNA-b6819/markers.fasta
[2023-03-18 10:41:34,043] [INFO] Task started: Blastn
[2023-03-18 10:41:34,043] [INFO] Running command: blastn -query OceanDNA-b6819/markers.fasta -db /var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference/reference_markers.fasta -out OceanDNA-b6819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:41:34,622] [INFO] Task succeeded: Blastn
[2023-03-18 10:41:34,623] [INFO] Selected 19 target genomes.
[2023-03-18 10:41:34,623] [INFO] Target genome list was writen to OceanDNA-b6819/target_genomes.txt
[2023-03-18 10:41:34,634] [INFO] Task started: fastANI
[2023-03-18 10:41:34,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg46888ce3-dcc6-42af-a682-65395152ed93/OceanDNA-b6819.fa --refList OceanDNA-b6819/target_genomes.txt --output OceanDNA-b6819/fastani_result.tsv --threads 1
[2023-03-18 10:41:46,148] [INFO] Task succeeded: fastANI
[2023-03-18 10:41:46,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:41:46,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:41:46,160] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:41:46,161] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:41:46,161] [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
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	92.7486	637	722	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.3598	333	722	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.2299	290	722	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	78.0362	296	722	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.0184	292	722	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	78.0054	296	722	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	78.0001	276	722	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	77.9711	230	722	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.9668	283	722	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.8647	317	722	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.812	301	722	95	below_threshold
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	77.7428	234	722	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	77.6975	254	722	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	77.669	236	722	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	77.4804	290	722	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.7729	149	722	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	76.693	160	722	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	76.6355	155	722	95	below_threshold
Flavobacterium chungbukense	strain=CS100	GCA_020805785.1	877464	877464	type	True	76.608	172	722	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:41:46,161] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6819/tc_result.tsv
[2023-03-18 10:41:46,161] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:41:46,161] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:41:46,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference/checkm_data
[2023-03-18 10:41:46,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:41:46,166] [INFO] Task started: CheckM
[2023-03-18 10:41:46,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6819/checkm_input OceanDNA-b6819/checkm_result
[2023-03-18 10:42:22,726] [INFO] Task succeeded: CheckM
[2023-03-18 10:42:22,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:42:22,751] [INFO] ===== Completeness check finished =====
[2023-03-18 10:42:22,751] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:42:22,751] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6819/markers.fasta)
[2023-03-18 10:42:22,752] [INFO] Task started: Blastn
[2023-03-18 10:42:22,752] [INFO] Running command: blastn -query OceanDNA-b6819/markers.fasta -db /var/lib/cwl/stga513daf1-e1cd-4d55-99d2-f46510c4bd8a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:42:23,565] [INFO] Task succeeded: Blastn
[2023-03-18 10:42:23,565] [INFO] Selected 15 target genomes.
[2023-03-18 10:42:23,566] [INFO] Target genome list was writen to OceanDNA-b6819/target_genomes_gtdb.txt
[2023-03-18 10:42:23,656] [INFO] Task started: fastANI
[2023-03-18 10:42:23,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg46888ce3-dcc6-42af-a682-65395152ed93/OceanDNA-b6819.fa --refList OceanDNA-b6819/target_genomes_gtdb.txt --output OceanDNA-b6819/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:42:32,040] [INFO] Task succeeded: fastANI
[2023-03-18 10:42:32,049] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:42:32,049] [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
GCF_000422685.1	s__Flavobacterium gelidilacus	92.7527	637	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	79.4856	303	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	78.3715	332	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	78.2678	314	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCA_002483315.1	s__Flavobacterium sp002483315	78.1116	287	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	78.0631	298	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363695.1	s__Flavobacterium cheniae	78.0054	296	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	77.9771	284	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108955.1	s__Flavobacterium terrigena	77.9719	230	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	77.9641	317	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	77.9628	266	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800945.1	s__Flavobacterium sp001800945	77.8845	152	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.6312	250	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401995.1	s__Flavobacterium sp018401995	77.6264	192	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	77.6051	252	722	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:42:32,050] [INFO] GTDB search result was written to OceanDNA-b6819/result_gtdb.tsv
[2023-03-18 10:42:32,050] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:42:32,052] [INFO] DFAST_QC result json was written to OceanDNA-b6819/dqc_result.json
[2023-03-18 10:42:32,052] [INFO] DFAST_QC completed!
[2023-03-18 10:42:32,052] [INFO] Total running time: 0h1m13s