[2023-03-17 23:20:45,988] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:20:45,989] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:20:45,989] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference
[2023-03-17 23:20:47,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:20:47,119] [INFO] Task started: Prodigal
[2023-03-17 23:20:47,119] [INFO] Running command: cat /var/lib/cwl/stg2b457b8f-329c-4e65-be76-2e1f5f8db821/OceanDNA-b38217.fa | prodigal -d OceanDNA-b38217/cds.fna -a OceanDNA-b38217/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:21:12,149] [INFO] Task succeeded: Prodigal
[2023-03-17 23:21:12,149] [INFO] Task started: HMMsearch
[2023-03-17 23:21:12,150] [INFO] Running command: hmmsearch --tblout OceanDNA-b38217/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference/reference_markers.hmm OceanDNA-b38217/protein.faa > /dev/null
[2023-03-17 23:21:12,373] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:21:12,374] [INFO] Found 6/6 markers.
[2023-03-17 23:21:12,401] [INFO] Query marker FASTA was written to OceanDNA-b38217/markers.fasta
[2023-03-17 23:21:12,402] [INFO] Task started: Blastn
[2023-03-17 23:21:12,402] [INFO] Running command: blastn -query OceanDNA-b38217/markers.fasta -db /var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference/reference_markers.fasta -out OceanDNA-b38217/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:21:13,084] [INFO] Task succeeded: Blastn
[2023-03-17 23:21:13,085] [INFO] Selected 11 target genomes.
[2023-03-17 23:21:13,085] [INFO] Target genome list was writen to OceanDNA-b38217/target_genomes.txt
[2023-03-17 23:21:13,092] [INFO] Task started: fastANI
[2023-03-17 23:21:13,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b457b8f-329c-4e65-be76-2e1f5f8db821/OceanDNA-b38217.fa --refList OceanDNA-b38217/target_genomes.txt --output OceanDNA-b38217/fastani_result.tsv --threads 1
[2023-03-17 23:21:22,660] [INFO] Task succeeded: fastANI
[2023-03-17 23:21:22,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:21:22,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:21:22,668] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:21:22,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:21:22,668] [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
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	85.4083	1069	1412	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	85.2352	1008	1412	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	84.6199	925	1412	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	84.6197	915	1412	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	83.2454	872	1412	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	82.2533	806	1412	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.9492	625	1412	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.9177	628	1412	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.7191	464	1412	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.1874	194	1412	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.084	209	1412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:21:22,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38217/tc_result.tsv
[2023-03-17 23:21:22,669] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:21:22,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:21:22,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference/checkm_data
[2023-03-17 23:21:22,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:21:22,675] [INFO] Task started: CheckM
[2023-03-17 23:21:22,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38217/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38217/checkm_input OceanDNA-b38217/checkm_result
[2023-03-17 23:22:24,279] [INFO] Task succeeded: CheckM
[2023-03-17 23:22:24,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:22:24,282] [INFO] ===== Completeness check finished =====
[2023-03-17 23:22:24,283] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:22:24,283] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38217/markers.fasta)
[2023-03-17 23:22:24,284] [INFO] Task started: Blastn
[2023-03-17 23:22:24,284] [INFO] Running command: blastn -query OceanDNA-b38217/markers.fasta -db /var/lib/cwl/stgbf86ff4d-4548-4705-a938-a45ca9f1261b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38217/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:22:25,430] [INFO] Task succeeded: Blastn
[2023-03-17 23:22:25,431] [INFO] Selected 10 target genomes.
[2023-03-17 23:22:25,431] [INFO] Target genome list was writen to OceanDNA-b38217/target_genomes_gtdb.txt
[2023-03-17 23:22:25,604] [INFO] Task started: fastANI
[2023-03-17 23:22:25,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b457b8f-329c-4e65-be76-2e1f5f8db821/OceanDNA-b38217.fa --refList OceanDNA-b38217/target_genomes_gtdb.txt --output OceanDNA-b38217/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:22:35,877] [INFO] Task succeeded: fastANI
[2023-03-17 23:22:35,884] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:22:35,884] [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_004295565.1	s__Halomonas olivaria	87.8483	1080	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211105.1	s__Halomonas campaniensis_A	87.797	1074	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_000336575.1	s__Halomonas titanicae	85.3998	1070	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_004364445.1	s__Halomonas alkaliantarctica	85.3922	1024	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_013416325.1	s__Halomonas sedimenti	85.2352	1008	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_002257525.1	s__Halomonas ventosae_B	84.8848	1040	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000236035.1	s__Halomonas boliviensis	84.6199	925	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001882345.1	s__Halomonas sp001882345	84.618	900	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651035.1	s__Halomonas sp001651035	84.5837	972	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
GCA_001507855.1	s__Halomonas sp001507855	81.7156	660	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:22:35,884] [INFO] GTDB search result was written to OceanDNA-b38217/result_gtdb.tsv
[2023-03-17 23:22:35,884] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:22:35,886] [INFO] DFAST_QC result json was written to OceanDNA-b38217/dqc_result.json
[2023-03-17 23:22:35,886] [INFO] DFAST_QC completed!
[2023-03-17 23:22:35,886] [INFO] Total running time: 0h1m50s