[2023-03-18 08:31:58,243] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:58,243] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:58,243] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference
[2023-03-18 08:31:59,339] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:59,339] [INFO] Task started: Prodigal
[2023-03-18 08:31:59,339] [INFO] Running command: cat /var/lib/cwl/stg6b6cbe9d-87a9-42f1-8acc-4ce2a79d82c5/OceanDNA-b24037.fa | prodigal -d OceanDNA-b24037/cds.fna -a OceanDNA-b24037/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:10,849] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:10,850] [INFO] Task started: HMMsearch
[2023-03-18 08:32:10,850] [INFO] Running command: hmmsearch --tblout OceanDNA-b24037/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference/reference_markers.hmm OceanDNA-b24037/protein.faa > /dev/null
[2023-03-18 08:32:11,022] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:11,022] [INFO] Found 6/6 markers.
[2023-03-18 08:32:11,040] [INFO] Query marker FASTA was written to OceanDNA-b24037/markers.fasta
[2023-03-18 08:32:11,040] [INFO] Task started: Blastn
[2023-03-18 08:32:11,040] [INFO] Running command: blastn -query OceanDNA-b24037/markers.fasta -db /var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference/reference_markers.fasta -out OceanDNA-b24037/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:11,672] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:11,673] [INFO] Selected 31 target genomes.
[2023-03-18 08:32:11,673] [INFO] Target genome list was writen to OceanDNA-b24037/target_genomes.txt
[2023-03-18 08:32:11,687] [INFO] Task started: fastANI
[2023-03-18 08:32:11,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b6cbe9d-87a9-42f1-8acc-4ce2a79d82c5/OceanDNA-b24037.fa --refList OceanDNA-b24037/target_genomes.txt --output OceanDNA-b24037/fastani_result.tsv --threads 1
[2023-03-18 08:32:29,947] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:29,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:29,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:29,951] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:29,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:32:29,951] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	77.6456	197	571	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	75.527	62	571	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	75.4921	64	571	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:29,951] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24037/tc_result.tsv
[2023-03-18 08:32:29,951] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:29,952] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:29,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference/checkm_data
[2023-03-18 08:32:29,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:30,095] [INFO] Task started: CheckM
[2023-03-18 08:32:30,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24037/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24037/checkm_input OceanDNA-b24037/checkm_result
[2023-03-18 08:33:02,954] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:02,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:02,957] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:02,957] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:02,957] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24037/markers.fasta)
[2023-03-18 08:33:02,957] [INFO] Task started: Blastn
[2023-03-18 08:33:02,958] [INFO] Running command: blastn -query OceanDNA-b24037/markers.fasta -db /var/lib/cwl/stgc9204369-a53e-41be-ac40-73915f0875f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24037/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:04,070] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:04,070] [INFO] Selected 22 target genomes.
[2023-03-18 08:33:04,071] [INFO] Target genome list was writen to OceanDNA-b24037/target_genomes_gtdb.txt
[2023-03-18 08:33:04,150] [INFO] Task started: fastANI
[2023-03-18 08:33:04,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b6cbe9d-87a9-42f1-8acc-4ce2a79d82c5/OceanDNA-b24037.fa --refList OceanDNA-b24037/target_genomes_gtdb.txt --output OceanDNA-b24037/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:17,457] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:17,463] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:33:17,463] [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_002943565.1	s__Marinicaulis flavus	77.6456	197	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	77.3664	166	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002388885.1	s__Marinicaulis sp002388885	77.2695	153	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.69	70	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_013151255.1	s__Marinicaulis sp013151255	76.0912	97	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	75.901	59	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	75.8242	73	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151435.1	s__Marinicaulis sp013151435	75.8143	63	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	97.18	97.18	0.82	0.82	2	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	75.527	62	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:17,463] [INFO] GTDB search result was written to OceanDNA-b24037/result_gtdb.tsv
[2023-03-18 08:33:17,463] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:17,464] [INFO] DFAST_QC result json was written to OceanDNA-b24037/dqc_result.json
[2023-03-18 08:33:17,464] [INFO] DFAST_QC completed!
[2023-03-18 08:33:17,464] [INFO] Total running time: 0h1m19s