[2023-03-19 01:55:26,636] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:55:26,636] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:55:26,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference
[2023-03-19 01:55:27,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:55:27,730] [INFO] Task started: Prodigal
[2023-03-19 01:55:27,730] [INFO] Running command: cat /var/lib/cwl/stgfd1b0ad0-562a-4259-af80-43c717f4034b/OceanDNA-b38215.fa | prodigal -d OceanDNA-b38215/cds.fna -a OceanDNA-b38215/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:55:51,894] [INFO] Task succeeded: Prodigal
[2023-03-19 01:55:51,894] [INFO] Task started: HMMsearch
[2023-03-19 01:55:51,894] [INFO] Running command: hmmsearch --tblout OceanDNA-b38215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference/reference_markers.hmm OceanDNA-b38215/protein.faa > /dev/null
[2023-03-19 01:55:52,109] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:55:52,110] [INFO] Found 6/6 markers.
[2023-03-19 01:55:52,139] [INFO] Query marker FASTA was written to OceanDNA-b38215/markers.fasta
[2023-03-19 01:55:52,141] [INFO] Task started: Blastn
[2023-03-19 01:55:52,141] [INFO] Running command: blastn -query OceanDNA-b38215/markers.fasta -db /var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference/reference_markers.fasta -out OceanDNA-b38215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:55:52,843] [INFO] Task succeeded: Blastn
[2023-03-19 01:55:52,844] [INFO] Selected 11 target genomes.
[2023-03-19 01:55:52,844] [INFO] Target genome list was writen to OceanDNA-b38215/target_genomes.txt
[2023-03-19 01:55:52,851] [INFO] Task started: fastANI
[2023-03-19 01:55:52,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd1b0ad0-562a-4259-af80-43c717f4034b/OceanDNA-b38215.fa --refList OceanDNA-b38215/target_genomes.txt --output OceanDNA-b38215/fastani_result.tsv --threads 1
[2023-03-19 01:56:02,996] [INFO] Task succeeded: fastANI
[2023-03-19 01:56:02,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:56:02,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:56:03,003] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 01:56:03,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 01:56:03,004] [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 maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	96.7982	1204	1345	95	conclusive
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	92.0809	1076	1345	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	84.8239	1005	1345	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	84.8211	1014	1345	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	84.1955	946	1345	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	84.18	955	1345	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.4733	690	1345	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.4189	700	1345	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.3128	502	1345	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.457	223	1345	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.3388	237	1345	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:56:03,006] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38215/tc_result.tsv
[2023-03-19 01:56:03,006] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:56:03,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:56:03,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference/checkm_data
[2023-03-19 01:56:03,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:56:03,021] [INFO] Task started: CheckM
[2023-03-19 01:56:03,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38215/checkm_input OceanDNA-b38215/checkm_result
[2023-03-19 01:57:02,554] [INFO] Task succeeded: CheckM
[2023-03-19 01:57:02,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:57:02,562] [INFO] ===== Completeness check finished =====
[2023-03-19 01:57:02,562] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:57:02,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38215/markers.fasta)
[2023-03-19 01:57:02,563] [INFO] Task started: Blastn
[2023-03-19 01:57:02,563] [INFO] Running command: blastn -query OceanDNA-b38215/markers.fasta -db /var/lib/cwl/stg3ae409f0-b700-421f-846e-6c41a43e2be9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:57:03,795] [INFO] Task succeeded: Blastn
[2023-03-19 01:57:03,795] [INFO] Selected 10 target genomes.
[2023-03-19 01:57:03,796] [INFO] Target genome list was writen to OceanDNA-b38215/target_genomes_gtdb.txt
[2023-03-19 01:57:03,802] [INFO] Task started: fastANI
[2023-03-19 01:57:03,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd1b0ad0-562a-4259-af80-43c717f4034b/OceanDNA-b38215.fa --refList OceanDNA-b38215/target_genomes_gtdb.txt --output OceanDNA-b38215/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:57:14,250] [INFO] Task succeeded: fastANI
[2023-03-19 01:57:14,256] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:57:14,256] [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_013371085.1	s__Halomonas maris	96.7982	1204	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000235725.1	s__Halomonas sp000235725	94.0893	1059	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCF_013415125.1	s__Halomonas glaciei	92.0665	1077	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCA_002366715.1	s__Halomonas sp002366715	87.4276	1066	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001882345.1	s__Halomonas sp001882345	85.1518	991	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007182875.1	s__Halomonas sulfidaeris	85.1076	996	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.07	97.07	0.89	0.89	2	-
GCF_000336575.1	s__Halomonas titanicae	84.8113	1015	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_002257525.1	s__Halomonas ventosae_B	84.7004	1013	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_004364445.1	s__Halomonas alkaliantarctica	84.6667	1013	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_000236035.1	s__Halomonas boliviensis	84.1698	956	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:57:14,257] [INFO] GTDB search result was written to OceanDNA-b38215/result_gtdb.tsv
[2023-03-19 01:57:14,258] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:57:14,260] [INFO] DFAST_QC result json was written to OceanDNA-b38215/dqc_result.json
[2023-03-19 01:57:14,260] [INFO] DFAST_QC completed!
[2023-03-19 01:57:14,261] [INFO] Total running time: 0h1m48s