[2023-03-15 13:20:51,556] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,556] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference
[2023-03-15 13:20:52,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,714] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,714] [INFO] Running command: cat /var/lib/cwl/stg153a6939-3768-4f45-acd8-3e8d0374906c/OceanDNA-b23643.fa | prodigal -d OceanDNA-b23643/cds.fna -a OceanDNA-b23643/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:11,593] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:11,594] [INFO] Task started: HMMsearch
[2023-03-15 13:21:11,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b23643/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference/reference_markers.hmm OceanDNA-b23643/protein.faa > /dev/null
[2023-03-15 13:21:11,816] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:11,816] [INFO] Found 6/6 markers.
[2023-03-15 13:21:11,839] [INFO] Query marker FASTA was written to OceanDNA-b23643/markers.fasta
[2023-03-15 13:21:11,841] [INFO] Task started: Blastn
[2023-03-15 13:21:11,841] [INFO] Running command: blastn -query OceanDNA-b23643/markers.fasta -db /var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference/reference_markers.fasta -out OceanDNA-b23643/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:12,742] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:12,743] [INFO] Selected 16 target genomes.
[2023-03-15 13:21:12,744] [INFO] Target genome list was writen to OceanDNA-b23643/target_genomes.txt
[2023-03-15 13:21:12,756] [INFO] Task started: fastANI
[2023-03-15 13:21:12,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg153a6939-3768-4f45-acd8-3e8d0374906c/OceanDNA-b23643.fa --refList OceanDNA-b23643/target_genomes.txt --output OceanDNA-b23643/fastani_result.tsv --threads 1
[2023-03-15 13:21:24,852] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:24,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:24,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:24,863] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:24,863] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:24,863] [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
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	79.3155	542	1029	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	79.0181	489	1029	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.2719	369	1029	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.1497	373	1029	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.1384	357	1029	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.1194	365	1029	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.0678	413	1029	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.9482	183	1029	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.8522	187	1029	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.5536	139	1029	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	76.2693	124	1029	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	76.2096	108	1029	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.0898	119	1029	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.991	108	1029	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	75.9426	126	1029	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	75.9007	118	1029	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:24,864] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23643/tc_result.tsv
[2023-03-15 13:21:24,864] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:24,864] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:24,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference/checkm_data
[2023-03-15 13:21:24,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:24,870] [INFO] Task started: CheckM
[2023-03-15 13:21:24,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23643/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23643/checkm_input OceanDNA-b23643/checkm_result
[2023-03-15 13:22:12,713] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:12,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:12,717] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:12,717] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:12,717] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23643/markers.fasta)
[2023-03-15 13:22:12,718] [INFO] Task started: Blastn
[2023-03-15 13:22:12,718] [INFO] Running command: blastn -query OceanDNA-b23643/markers.fasta -db /var/lib/cwl/stg04cc6237-75e1-4f47-810b-ba85f9b9d1ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23643/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:14,340] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:14,342] [INFO] Selected 8 target genomes.
[2023-03-15 13:22:14,342] [INFO] Target genome list was writen to OceanDNA-b23643/target_genomes_gtdb.txt
[2023-03-15 13:22:14,369] [INFO] Task started: fastANI
[2023-03-15 13:22:14,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg153a6939-3768-4f45-acd8-3e8d0374906c/OceanDNA-b23643.fa --refList OceanDNA-b23643/target_genomes_gtdb.txt --output OceanDNA-b23643/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:19,958] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:19,964] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:22:19,964] [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_016124495.1	s__Hyphomonas sp016124495	94.083	811	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464545.1	s__Hyphomonas sp001464545	89.8455	768	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.95	98.95	0.94	0.94	2	-
GCA_013791775.1	s__Hyphomonas sp013791775	82.5055	677	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.98	99.96	1.00	0.99	4	-
GCA_016712445.1	s__Hyphomonas sp016712445	82.3239	702	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125515.1	s__Hyphomonas sp016125515	81.7903	668	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486945.1	s__Hyphomonas sp003486945	80.9028	441	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282565.1	s__Hyphomonas sp002282565	79.2333	385	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	77.2355	87	1029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:19,965] [INFO] GTDB search result was written to OceanDNA-b23643/result_gtdb.tsv
[2023-03-15 13:22:19,965] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:19,967] [INFO] DFAST_QC result json was written to OceanDNA-b23643/dqc_result.json
[2023-03-15 13:22:19,967] [INFO] DFAST_QC completed!
[2023-03-15 13:22:19,967] [INFO] Total running time: 0h1m28s