[2023-03-15 17:46:31,608] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,611] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,611] [INFO] DQC Reference Directory: /var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference
[2023-03-15 17:46:32,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,850] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,850] [INFO] Running command: cat /var/lib/cwl/stgf7fa02d2-98d9-45f0-8ab6-0d8dd416f276/OceanDNA-b23527.fa | prodigal -d OceanDNA-b23527/cds.fna -a OceanDNA-b23527/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:42,989] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:42,990] [INFO] Task started: HMMsearch
[2023-03-15 17:46:42,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b23527/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference/reference_markers.hmm OceanDNA-b23527/protein.faa > /dev/null
[2023-03-15 17:46:43,171] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:43,172] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf7fa02d2-98d9-45f0-8ab6-0d8dd416f276/OceanDNA-b23527.fa]
[2023-03-15 17:46:43,215] [INFO] Query marker FASTA was written to OceanDNA-b23527/markers.fasta
[2023-03-15 17:46:43,215] [INFO] Task started: Blastn
[2023-03-15 17:46:43,215] [INFO] Running command: blastn -query OceanDNA-b23527/markers.fasta -db /var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference/reference_markers.fasta -out OceanDNA-b23527/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:43,950] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:43,957] [INFO] Selected 19 target genomes.
[2023-03-15 17:46:43,958] [INFO] Target genome list was writen to OceanDNA-b23527/target_genomes.txt
[2023-03-15 17:46:43,968] [INFO] Task started: fastANI
[2023-03-15 17:46:43,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7fa02d2-98d9-45f0-8ab6-0d8dd416f276/OceanDNA-b23527.fa --refList OceanDNA-b23527/target_genomes.txt --output OceanDNA-b23527/fastani_result.tsv --threads 1
[2023-03-15 17:46:56,362] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:56,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:56,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:56,369] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:46:56,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:46:56,370] [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	97.422	489	517	95	conclusive
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	80.7148	324	517	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	79.3193	267	517	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	79.2922	270	517	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	78.6164	231	517	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	78.5566	252	517	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	78.4828	218	517	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	77.4796	143	517	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.145	115	517	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.9631	136	517	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	75.4544	51	517	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:46:56,373] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23527/tc_result.tsv
[2023-03-15 17:46:56,377] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:56,378] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:56,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference/checkm_data
[2023-03-15 17:46:56,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:56,385] [INFO] Task started: CheckM
[2023-03-15 17:46:56,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23527/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23527/checkm_input OceanDNA-b23527/checkm_result
[2023-03-15 17:47:26,751] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:26,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:26,756] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:26,756] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:26,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23527/markers.fasta)
[2023-03-15 17:47:26,757] [INFO] Task started: Blastn
[2023-03-15 17:47:26,757] [INFO] Running command: blastn -query OceanDNA-b23527/markers.fasta -db /var/lib/cwl/stga14510b1-1ccf-46b7-8ca6-e9099281219d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23527/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:28,075] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:28,077] [INFO] Selected 17 target genomes.
[2023-03-15 17:47:28,078] [INFO] Target genome list was writen to OceanDNA-b23527/target_genomes_gtdb.txt
[2023-03-15 17:47:28,095] [INFO] Task started: fastANI
[2023-03-15 17:47:28,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7fa02d2-98d9-45f0-8ab6-0d8dd416f276/OceanDNA-b23527.fa --refList OceanDNA-b23527/target_genomes_gtdb.txt --output OceanDNA-b23527/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:39,278] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:39,288] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:47:39,289] [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_003576285.1	s__Henriciella sp003576285	97.9717	501	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	conclusive
GCF_002088975.1	s__Henriciella aquimarina	80.709	323	517	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	79.3206	249	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_002088945.1	s__Henriciella pelagia	79.3193	267	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012960415.1	s__Henriciella sp012960415	79.0224	245	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_002088935.1	s__Henriciella litoralis	78.5982	232	517	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	78.5733	251	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682735.1	s__Hyphomonas sp000682735	77.7349	140	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_002700305.1	s__Hyphomonas sp002700305	77.4427	138	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
GCA_000961795.1	s__Hyphomonas sp000961795	77.3914	135	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792385.1	s__Hyphomonas sp017792385	77.3629	133	517	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	77.0497	111	517	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	76.9903	143	517	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	76.9813	135	517	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 17:47:39,291] [INFO] GTDB search result was written to OceanDNA-b23527/result_gtdb.tsv
[2023-03-15 17:47:39,292] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:39,296] [INFO] DFAST_QC result json was written to OceanDNA-b23527/dqc_result.json
[2023-03-15 17:47:39,296] [INFO] DFAST_QC completed!
[2023-03-15 17:47:39,296] [INFO] Total running time: 0h1m8s