[2023-03-18 23:27:53,715] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference
[2023-03-18 23:27:55,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,549] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,549] [INFO] Running command: cat /var/lib/cwl/stga8c8865b-a42c-44f6-b01a-14a4129feefb/OceanDNA-b23508.fa | prodigal -d OceanDNA-b23508/cds.fna -a OceanDNA-b23508/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:14,464] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:14,465] [INFO] Task started: HMMsearch
[2023-03-18 23:28:14,465] [INFO] Running command: hmmsearch --tblout OceanDNA-b23508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference/reference_markers.hmm OceanDNA-b23508/protein.faa > /dev/null
[2023-03-18 23:28:14,671] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:14,672] [INFO] Found 6/6 markers.
[2023-03-18 23:28:14,692] [INFO] Query marker FASTA was written to OceanDNA-b23508/markers.fasta
[2023-03-18 23:28:14,693] [INFO] Task started: Blastn
[2023-03-18 23:28:14,693] [INFO] Running command: blastn -query OceanDNA-b23508/markers.fasta -db /var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference/reference_markers.fasta -out OceanDNA-b23508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:15,352] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:15,353] [INFO] Selected 23 target genomes.
[2023-03-18 23:28:15,353] [INFO] Target genome list was writen to OceanDNA-b23508/target_genomes.txt
[2023-03-18 23:28:15,369] [INFO] Task started: fastANI
[2023-03-18 23:28:15,370] [INFO] Running command: fastANI --query /var/lib/cwl/stga8c8865b-a42c-44f6-b01a-14a4129feefb/OceanDNA-b23508.fa --refList OceanDNA-b23508/target_genomes.txt --output OceanDNA-b23508/fastani_result.tsv --threads 1
[2023-03-18 23:28:28,513] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:28,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:28,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:28,521] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:28,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:28,521] [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 pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.4962	60	1022	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.4465	64	1022	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.4385	81	1022	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.3146	75	1022	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.225	70	1022	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.1602	74	1022	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.0622	84	1022	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.043	84	1022	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	75.7282	64	1022	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:28,521] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23508/tc_result.tsv
[2023-03-18 23:28:28,521] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:28,521] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:28,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference/checkm_data
[2023-03-18 23:28:28,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:28,530] [INFO] Task started: CheckM
[2023-03-18 23:28:28,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23508/checkm_input OceanDNA-b23508/checkm_result
[2023-03-18 23:29:17,508] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:17,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:17,511] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:17,511] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:17,512] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23508/markers.fasta)
[2023-03-18 23:29:17,513] [INFO] Task started: Blastn
[2023-03-18 23:29:17,513] [INFO] Running command: blastn -query OceanDNA-b23508/markers.fasta -db /var/lib/cwl/stg23b46844-a2a4-4208-a819-ff4dee855a61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:29:18,590] [INFO] Task succeeded: Blastn
[2023-03-18 23:29:18,591] [INFO] Selected 17 target genomes.
[2023-03-18 23:29:18,591] [INFO] Target genome list was writen to OceanDNA-b23508/target_genomes_gtdb.txt
[2023-03-18 23:29:18,607] [INFO] Task started: fastANI
[2023-03-18 23:29:18,608] [INFO] Running command: fastANI --query /var/lib/cwl/stga8c8865b-a42c-44f6-b01a-14a4129feefb/OceanDNA-b23508.fa --refList OceanDNA-b23508/target_genomes_gtdb.txt --output OceanDNA-b23508/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:29,035] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:29,044] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:29:29,044] [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_013213785.1	s__Henriciella sp013213785	99.8756	1010	1022	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_013214545.1	s__Henriciella sp013214545	78.3723	373	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213825.1	s__Henriciella sp013213825	78.2384	340	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854405.1	s__Henriciella sp001854405	78.2244	352	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642885.1	s__Henriciella sp017642885	78.0477	330	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCA_012960415.1	s__Henriciella sp012960415	76.311	83	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_000682735.1	s__Hyphomonas sp000682735	76.198	60	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCF_003576245.1	s__Henriciella algicola	76.043	84	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763715.1	s__Hyphomonas sp014763715	76.0025	53	1022	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	75.961	56	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	75.8275	73	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_000682755.1	s__Hyphomonas beringensis	75.7282	64	1022	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	75.4587	57	1022	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 23:29:29,044] [INFO] GTDB search result was written to OceanDNA-b23508/result_gtdb.tsv
[2023-03-18 23:29:29,044] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:29,045] [INFO] DFAST_QC result json was written to OceanDNA-b23508/dqc_result.json
[2023-03-18 23:29:29,046] [INFO] DFAST_QC completed!
[2023-03-18 23:29:29,046] [INFO] Total running time: 0h1m35s