[2023-03-18 04:38:00,389] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,389] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,389] [INFO] DQC Reference Directory: /var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference
[2023-03-18 04:38:01,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,503] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,503] [INFO] Running command: cat /var/lib/cwl/stga180a127-a95d-43b2-9446-672a55f6fad4/OceanDNA-b23655.fa | prodigal -d OceanDNA-b23655/cds.fna -a OceanDNA-b23655/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:18,025] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:18,025] [INFO] Task started: HMMsearch
[2023-03-18 04:38:18,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b23655/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference/reference_markers.hmm OceanDNA-b23655/protein.faa > /dev/null
[2023-03-18 04:38:18,220] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:18,221] [INFO] Found 6/6 markers.
[2023-03-18 04:38:18,239] [INFO] Query marker FASTA was written to OceanDNA-b23655/markers.fasta
[2023-03-18 04:38:18,241] [INFO] Task started: Blastn
[2023-03-18 04:38:18,241] [INFO] Running command: blastn -query OceanDNA-b23655/markers.fasta -db /var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference/reference_markers.fasta -out OceanDNA-b23655/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:18,958] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:18,959] [INFO] Selected 19 target genomes.
[2023-03-18 04:38:18,959] [INFO] Target genome list was writen to OceanDNA-b23655/target_genomes.txt
[2023-03-18 04:38:18,972] [INFO] Task started: fastANI
[2023-03-18 04:38:18,973] [INFO] Running command: fastANI --query /var/lib/cwl/stga180a127-a95d-43b2-9446-672a55f6fad4/OceanDNA-b23655.fa --refList OceanDNA-b23655/target_genomes.txt --output OceanDNA-b23655/fastani_result.tsv --threads 1
[2023-03-18 04:38:32,267] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:32,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:32,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:32,275] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:38:32,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:38:32,275] [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 atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	99.3219	832	868	95	conclusive
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	79.342	452	868	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	79.2288	419	868	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.1778	341	868	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.1742	311	868	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.7268	297	868	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	77.693	278	868	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	77.4766	264	868	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.2937	213	868	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.7001	147	868	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.6587	146	868	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:38:32,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23655/tc_result.tsv
[2023-03-18 04:38:32,276] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:32,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:32,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference/checkm_data
[2023-03-18 04:38:32,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:32,281] [INFO] Task started: CheckM
[2023-03-18 04:38:32,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23655/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23655/checkm_input OceanDNA-b23655/checkm_result
[2023-03-18 04:39:15,740] [INFO] Task succeeded: CheckM
[2023-03-18 04:39:15,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:39:15,742] [INFO] ===== Completeness check finished =====
[2023-03-18 04:39:15,742] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:39:15,742] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23655/markers.fasta)
[2023-03-18 04:39:15,743] [INFO] Task started: Blastn
[2023-03-18 04:39:15,743] [INFO] Running command: blastn -query OceanDNA-b23655/markers.fasta -db /var/lib/cwl/stgc810abbe-d3c4-4298-ac3c-92768825c8e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23655/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:16,984] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:16,986] [INFO] Selected 13 target genomes.
[2023-03-18 04:39:16,986] [INFO] Target genome list was writen to OceanDNA-b23655/target_genomes_gtdb.txt
[2023-03-18 04:39:16,997] [INFO] Task started: fastANI
[2023-03-18 04:39:16,997] [INFO] Running command: fastANI --query /var/lib/cwl/stga180a127-a95d-43b2-9446-672a55f6fad4/OceanDNA-b23655.fa --refList OceanDNA-b23655/target_genomes_gtdb.txt --output OceanDNA-b23655/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:39:25,754] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:25,762] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:39:25,762] [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_000682715.1	s__Hyphomonas atlantica	99.3219	832	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	conclusive
GCA_017792385.1	s__Hyphomonas sp017792385	82.3488	604	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414505.1	s__Hyphomonas sp002414505	81.0332	500	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCF_000682775.1	s__Hyphomonas sp000682775	80.7652	574	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCA_018222605.1	s__Hyphomonas sp002695785	79.5828	434	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682755.1	s__Hyphomonas beringensis	79.348	451	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682675.1	s__Hyphomonas pacifica	79.2288	419	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCA_014763715.1	s__Hyphomonas sp014763715	78.3234	308	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961695.1	s__Hyphomonas sp000961695	78.0757	312	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	77.7621	265	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	77.4883	263	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830285.1	s__Hyphomonas sp018830285	77.4859	255	868	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	76.703	161	868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:39:25,762] [INFO] GTDB search result was written to OceanDNA-b23655/result_gtdb.tsv
[2023-03-18 04:39:25,763] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:39:25,764] [INFO] DFAST_QC result json was written to OceanDNA-b23655/dqc_result.json
[2023-03-18 04:39:25,764] [INFO] DFAST_QC completed!
[2023-03-18 04:39:25,764] [INFO] Total running time: 0h1m25s