[2023-03-19 02:51:48,305] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:51:48,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:51:48,305] [INFO] DQC Reference Directory: /var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference
[2023-03-19 02:51:49,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:51:49,390] [INFO] Task started: Prodigal
[2023-03-19 02:51:49,390] [INFO] Running command: cat /var/lib/cwl/stg2ef9a6df-6e78-42c7-af16-9e8405206c52/OceanDNA-b23523.fa | prodigal -d OceanDNA-b23523/cds.fna -a OceanDNA-b23523/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:52:03,418] [INFO] Task succeeded: Prodigal
[2023-03-19 02:52:03,419] [INFO] Task started: HMMsearch
[2023-03-19 02:52:03,419] [INFO] Running command: hmmsearch --tblout OceanDNA-b23523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference/reference_markers.hmm OceanDNA-b23523/protein.faa > /dev/null
[2023-03-19 02:52:03,595] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:52:03,596] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ef9a6df-6e78-42c7-af16-9e8405206c52/OceanDNA-b23523.fa]
[2023-03-19 02:52:03,621] [INFO] Query marker FASTA was written to OceanDNA-b23523/markers.fasta
[2023-03-19 02:52:03,621] [INFO] Task started: Blastn
[2023-03-19 02:52:03,621] [INFO] Running command: blastn -query OceanDNA-b23523/markers.fasta -db /var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference/reference_markers.fasta -out OceanDNA-b23523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:04,303] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:04,303] [INFO] Selected 15 target genomes.
[2023-03-19 02:52:04,304] [INFO] Target genome list was writen to OceanDNA-b23523/target_genomes.txt
[2023-03-19 02:52:04,312] [INFO] Task started: fastANI
[2023-03-19 02:52:04,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef9a6df-6e78-42c7-af16-9e8405206c52/OceanDNA-b23523.fa --refList OceanDNA-b23523/target_genomes.txt --output OceanDNA-b23523/fastani_result.tsv --threads 1
[2023-03-19 02:52:14,377] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:14,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:52:14,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:52:14,385] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 02:52:14,386] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 02:52:14,386] [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 algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	95.2175	732	766	95	conclusive
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	85.7157	670	766	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	81.6703	549	766	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	79.0199	389	766	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	78.7933	359	766	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	78.4593	395	766	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	78.4478	334	766	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.082	166	766	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.7815	164	766	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	76.6136	135	766	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.379	134	766	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	76.219	52	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:52:14,393] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23523/tc_result.tsv
[2023-03-19 02:52:14,396] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:52:14,396] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:52:14,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference/checkm_data
[2023-03-19 02:52:14,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:52:14,401] [INFO] Task started: CheckM
[2023-03-19 02:52:14,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23523/checkm_input OceanDNA-b23523/checkm_result
[2023-03-19 02:52:52,840] [INFO] Task succeeded: CheckM
[2023-03-19 02:52:52,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:52:52,906] [INFO] ===== Completeness check finished =====
[2023-03-19 02:52:52,906] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:52:52,906] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23523/markers.fasta)
[2023-03-19 02:52:52,906] [INFO] Task started: Blastn
[2023-03-19 02:52:52,906] [INFO] Running command: blastn -query OceanDNA-b23523/markers.fasta -db /var/lib/cwl/stga101042d-a3c3-4a6b-b1d9-801224ec5233/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:54,051] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:54,051] [INFO] Selected 9 target genomes.
[2023-03-19 02:52:54,052] [INFO] Target genome list was writen to OceanDNA-b23523/target_genomes_gtdb.txt
[2023-03-19 02:52:54,060] [INFO] Task started: fastANI
[2023-03-19 02:52:54,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef9a6df-6e78-42c7-af16-9e8405206c52/OceanDNA-b23523.fa --refList OceanDNA-b23523/target_genomes_gtdb.txt --output OceanDNA-b23523/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:53:00,280] [INFO] Task succeeded: fastANI
[2023-03-19 02:53:00,286] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:53:00,286] [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_003576245.1	s__Henriciella algicola	95.2175	732	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012960415.1	s__Henriciella sp012960415	89.4203	687	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003576345.1	s__Henriciella barbarensis	85.7157	670	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376805.1	s__Henriciella marina	81.6442	551	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733705.1	s__Henriciella sp002733705	80.8914	504	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_003576285.1	s__Henriciella sp003576285	78.6876	367	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_002088935.1	s__Henriciella litoralis	78.4593	395	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	77.082	166	766	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	76.7724	147	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:53:00,286] [INFO] GTDB search result was written to OceanDNA-b23523/result_gtdb.tsv
[2023-03-19 02:53:00,286] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:53:00,287] [INFO] DFAST_QC result json was written to OceanDNA-b23523/dqc_result.json
[2023-03-19 02:53:00,288] [INFO] DFAST_QC completed!
[2023-03-19 02:53:00,288] [INFO] Total running time: 0h1m12s