[2023-03-19 00:39:47,223] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:39:47,224] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:39:47,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference
[2023-03-19 00:39:50,231] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:39:50,231] [INFO] Task started: Prodigal
[2023-03-19 00:39:50,231] [INFO] Running command: cat /var/lib/cwl/stg0c55a7c1-cd22-4789-a665-9771a84a2f15/OceanDNA-b6818.fa | prodigal -d OceanDNA-b6818/cds.fna -a OceanDNA-b6818/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:40:06,055] [INFO] Task succeeded: Prodigal
[2023-03-19 00:40:06,055] [INFO] Task started: HMMsearch
[2023-03-19 00:40:06,055] [INFO] Running command: hmmsearch --tblout OceanDNA-b6818/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference/reference_markers.hmm OceanDNA-b6818/protein.faa > /dev/null
[2023-03-19 00:40:06,222] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:40:06,223] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0c55a7c1-cd22-4789-a665-9771a84a2f15/OceanDNA-b6818.fa]
[2023-03-19 00:40:06,244] [INFO] Query marker FASTA was written to OceanDNA-b6818/markers.fasta
[2023-03-19 00:40:06,245] [INFO] Task started: Blastn
[2023-03-19 00:40:06,246] [INFO] Running command: blastn -query OceanDNA-b6818/markers.fasta -db /var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference/reference_markers.fasta -out OceanDNA-b6818/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:40:06,784] [INFO] Task succeeded: Blastn
[2023-03-19 00:40:06,787] [INFO] Selected 15 target genomes.
[2023-03-19 00:40:06,787] [INFO] Target genome list was writen to OceanDNA-b6818/target_genomes.txt
[2023-03-19 00:40:06,797] [INFO] Task started: fastANI
[2023-03-19 00:40:06,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c55a7c1-cd22-4789-a665-9771a84a2f15/OceanDNA-b6818.fa --refList OceanDNA-b6818/target_genomes.txt --output OceanDNA-b6818/fastani_result.tsv --threads 1
[2023-03-19 00:40:15,913] [INFO] Task succeeded: fastANI
[2023-03-19 00:40:15,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:40:15,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:40:15,923] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:40:15,923] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:40:15,923] [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	89.0707	716	844	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	79.0239	378	844	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.8944	380	844	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.8222	352	844	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	78.6821	338	844	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	78.6554	338	844	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.6524	315	844	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.4416	341	844	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	78.4415	278	844	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	78.3838	335	844	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	78.3526	327	844	95	below_threshold
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	78.227	289	844	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.083	314	844	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.4832	184	844	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.7391	108	844	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:40:15,924] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6818/tc_result.tsv
[2023-03-19 00:40:15,925] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:40:15,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:40:15,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference/checkm_data
[2023-03-19 00:40:15,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:40:15,930] [INFO] Task started: CheckM
[2023-03-19 00:40:15,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6818/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6818/checkm_input OceanDNA-b6818/checkm_result
[2023-03-19 00:40:57,116] [INFO] Task succeeded: CheckM
[2023-03-19 00:40:57,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:40:57,125] [INFO] ===== Completeness check finished =====
[2023-03-19 00:40:57,126] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:40:57,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6818/markers.fasta)
[2023-03-19 00:40:57,127] [INFO] Task started: Blastn
[2023-03-19 00:40:57,127] [INFO] Running command: blastn -query OceanDNA-b6818/markers.fasta -db /var/lib/cwl/stg58c9ac28-5a10-405a-8aa5-1afe7295ae5f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6818/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:40:57,903] [INFO] Task succeeded: Blastn
[2023-03-19 00:40:57,907] [INFO] Selected 15 target genomes.
[2023-03-19 00:40:57,907] [INFO] Target genome list was writen to OceanDNA-b6818/target_genomes_gtdb.txt
[2023-03-19 00:40:57,925] [INFO] Task started: fastANI
[2023-03-19 00:40:57,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c55a7c1-cd22-4789-a665-9771a84a2f15/OceanDNA-b6818.fa --refList OceanDNA-b6818/target_genomes_gtdb.txt --output OceanDNA-b6818/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:41:06,209] [INFO] Task succeeded: fastANI
[2023-03-19 00:41:06,218] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:41:06,218] [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	89.0833	715	844	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	80.0811	348	844	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	78.9147	374	844	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	78.9018	351	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_006491595.2	s__Flavobacterium jejuense	78.883	381	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	78.7699	326	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002483315.1	s__Flavobacterium sp002483315	78.7373	321	844	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	78.6277	293	844	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	78.6157	334	844	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	78.4508	278	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422095.1	s__Flavobacterium sp002422095	78.3897	251	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963025.1	s__Flavobacterium sp003963025	78.3112	225	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.0948	313	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001800945.1	s__Flavobacterium sp001800945	78.0399	171	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	77.2449	152	844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:41:06,219] [INFO] GTDB search result was written to OceanDNA-b6818/result_gtdb.tsv
[2023-03-19 00:41:06,219] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:41:06,222] [INFO] DFAST_QC result json was written to OceanDNA-b6818/dqc_result.json
[2023-03-19 00:41:06,222] [INFO] DFAST_QC completed!
[2023-03-19 00:41:06,222] [INFO] Total running time: 0h1m19s