[2023-03-15 21:57:40,277] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:57:40,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:57:40,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference
[2023-03-15 21:57:41,417] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:57:41,418] [INFO] Task started: Prodigal
[2023-03-15 21:57:41,418] [INFO] Running command: cat /var/lib/cwl/stg27ce6405-39cf-4787-a6b4-6e7b6cbc66ef/OceanDNA-b23522.fa | prodigal -d OceanDNA-b23522/cds.fna -a OceanDNA-b23522/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:57:49,132] [INFO] Task succeeded: Prodigal
[2023-03-15 21:57:49,132] [INFO] Task started: HMMsearch
[2023-03-15 21:57:49,132] [INFO] Running command: hmmsearch --tblout OceanDNA-b23522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference/reference_markers.hmm OceanDNA-b23522/protein.faa > /dev/null
[2023-03-15 21:57:49,291] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:57:49,292] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg27ce6405-39cf-4787-a6b4-6e7b6cbc66ef/OceanDNA-b23522.fa]
[2023-03-15 21:57:49,310] [INFO] Query marker FASTA was written to OceanDNA-b23522/markers.fasta
[2023-03-15 21:57:49,312] [INFO] Task started: Blastn
[2023-03-15 21:57:49,312] [INFO] Running command: blastn -query OceanDNA-b23522/markers.fasta -db /var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference/reference_markers.fasta -out OceanDNA-b23522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:57:49,834] [INFO] Task succeeded: Blastn
[2023-03-15 21:57:49,836] [INFO] Selected 16 target genomes.
[2023-03-15 21:57:49,836] [INFO] Target genome list was writen to OceanDNA-b23522/target_genomes.txt
[2023-03-15 21:57:49,871] [INFO] Task started: fastANI
[2023-03-15 21:57:49,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ce6405-39cf-4787-a6b4-6e7b6cbc66ef/OceanDNA-b23522.fa --refList OceanDNA-b23522/target_genomes.txt --output OceanDNA-b23522/fastani_result.tsv --threads 1
[2023-03-15 21:57:58,974] [INFO] Task succeeded: fastANI
[2023-03-15 21:57:58,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:57:58,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:57:58,982] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:57:58,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:57:58,983] [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
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.7333	85	321	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	77.7215	75	321	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	77.6779	76	321	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	77.597	96	321	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	77.3306	87	321	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.299	88	321	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	77.123	67	321	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	77.0363	92	321	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.702	54	321	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.529	53	321	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:57:58,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23522/tc_result.tsv
[2023-03-15 21:57:58,990] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:57:58,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:57:58,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference/checkm_data
[2023-03-15 21:57:58,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:57:59,071] [INFO] Task started: CheckM
[2023-03-15 21:57:59,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23522/checkm_input OceanDNA-b23522/checkm_result
[2023-03-15 21:58:24,156] [INFO] Task succeeded: CheckM
[2023-03-15 21:58:24,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:58:24,203] [INFO] ===== Completeness check finished =====
[2023-03-15 21:58:24,203] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:58:24,203] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23522/markers.fasta)
[2023-03-15 21:58:24,204] [INFO] Task started: Blastn
[2023-03-15 21:58:24,204] [INFO] Running command: blastn -query OceanDNA-b23522/markers.fasta -db /var/lib/cwl/stg8c651256-fa9d-4776-bd3a-f395e1238dda/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:58:24,931] [INFO] Task succeeded: Blastn
[2023-03-15 21:58:24,966] [INFO] Selected 17 target genomes.
[2023-03-15 21:58:24,966] [INFO] Target genome list was writen to OceanDNA-b23522/target_genomes_gtdb.txt
[2023-03-15 21:58:25,218] [INFO] Task started: fastANI
[2023-03-15 21:58:25,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ce6405-39cf-4787-a6b4-6e7b6cbc66ef/OceanDNA-b23522.fa --refList OceanDNA-b23522/target_genomes_gtdb.txt --output OceanDNA-b23522/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:58:35,184] [INFO] Task succeeded: fastANI
[2023-03-15 21:58:35,191] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:58:35,191] [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_002088945.1	s__Henriciella pelagia	77.6779	76	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002088935.1	s__Henriciella litoralis	77.597	96	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576245.1	s__Henriciella algicola	77.3306	87	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	77.299	88	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	77.268	87	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_000376805.1	s__Henriciella marina	77.0363	92	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960415.1	s__Henriciella sp012960415	77.0238	90	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_000685295.1	s__Hyphomonas oceanitis	76.702	54	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	76.529	53	321	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	76.2587	52	321	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:58:35,193] [INFO] GTDB search result was written to OceanDNA-b23522/result_gtdb.tsv
[2023-03-15 21:58:35,196] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:58:35,197] [INFO] DFAST_QC result json was written to OceanDNA-b23522/dqc_result.json
[2023-03-15 21:58:35,197] [INFO] DFAST_QC completed!
[2023-03-15 21:58:35,197] [INFO] Total running time: 0h0m55s