[2023-03-18 01:35:16,896] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:35:16,897] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:35:16,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference
[2023-03-18 01:35:18,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:35:18,358] [INFO] Task started: Prodigal
[2023-03-18 01:35:18,358] [INFO] Running command: cat /var/lib/cwl/stg92bcda18-990c-4e9c-9ea4-b9ed02dea573/OceanDNA-b23832.fa | prodigal -d OceanDNA-b23832/cds.fna -a OceanDNA-b23832/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:35:25,550] [INFO] Task succeeded: Prodigal
[2023-03-18 01:35:25,551] [INFO] Task started: HMMsearch
[2023-03-18 01:35:25,551] [INFO] Running command: hmmsearch --tblout OceanDNA-b23832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference/reference_markers.hmm OceanDNA-b23832/protein.faa > /dev/null
[2023-03-18 01:35:25,704] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:35:25,705] [INFO] Found 6/6 markers.
[2023-03-18 01:35:25,723] [INFO] Query marker FASTA was written to OceanDNA-b23832/markers.fasta
[2023-03-18 01:35:25,724] [INFO] Task started: Blastn
[2023-03-18 01:35:25,724] [INFO] Running command: blastn -query OceanDNA-b23832/markers.fasta -db /var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference/reference_markers.fasta -out OceanDNA-b23832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:35:26,358] [INFO] Task succeeded: Blastn
[2023-03-18 01:35:26,359] [INFO] Selected 38 target genomes.
[2023-03-18 01:35:26,359] [INFO] Target genome list was writen to OceanDNA-b23832/target_genomes.txt
[2023-03-18 01:35:26,384] [INFO] Task started: fastANI
[2023-03-18 01:35:26,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg92bcda18-990c-4e9c-9ea4-b9ed02dea573/OceanDNA-b23832.fa --refList OceanDNA-b23832/target_genomes.txt --output OceanDNA-b23832/fastani_result.tsv --threads 1
[2023-03-18 01:35:49,080] [INFO] Task succeeded: fastANI
[2023-03-18 01:35:49,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:35:49,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:35:49,081] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:35:49,081] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:35:49,081] [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
--------------------------------------------------------------------------------
[2023-03-18 01:35:49,082] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23832/tc_result.tsv
[2023-03-18 01:35:49,083] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:35:49,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:35:49,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference/checkm_data
[2023-03-18 01:35:49,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:35:49,511] [INFO] Task started: CheckM
[2023-03-18 01:35:49,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23832/checkm_input OceanDNA-b23832/checkm_result
[2023-03-18 01:36:13,022] [INFO] Task succeeded: CheckM
[2023-03-18 01:36:13,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.37%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 01:36:13,026] [INFO] ===== Completeness check finished =====
[2023-03-18 01:36:13,026] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:36:13,027] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23832/markers.fasta)
[2023-03-18 01:36:13,028] [INFO] Task started: Blastn
[2023-03-18 01:36:13,028] [INFO] Running command: blastn -query OceanDNA-b23832/markers.fasta -db /var/lib/cwl/stgb328b45b-540b-40ca-ae96-53feb715d695/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:36:14,100] [INFO] Task succeeded: Blastn
[2023-03-18 01:36:14,102] [INFO] Selected 19 target genomes.
[2023-03-18 01:36:14,102] [INFO] Target genome list was writen to OceanDNA-b23832/target_genomes_gtdb.txt
[2023-03-18 01:36:14,118] [INFO] Task started: fastANI
[2023-03-18 01:36:14,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg92bcda18-990c-4e9c-9ea4-b9ed02dea573/OceanDNA-b23832.fa --refList OceanDNA-b23832/target_genomes_gtdb.txt --output OceanDNA-b23832/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:36:23,544] [INFO] Task succeeded: fastANI
[2023-03-18 01:36:23,553] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:36:23,553] [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_902826145.1	s__Terricaulis sp902826145	79.316	125	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464425.1	s__Terricaulis sp001464425	79.1958	102	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083515.1	s__Terricaulis sp002083515	79.1668	107	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792355.1	s__Terricaulis silvestris	79.0651	112	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791385.1	s__Terricaulis sp016791385	79.0349	83	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696695.1	s__Terricaulis sp900696695	79.0322	111	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	99.53	99.53	0.91	0.91	2	-
GCA_016703335.1	s__Terricaulis sp016703335	78.9007	113	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	97.50	97.50	0.87	0.87	2	-
GCA_017303355.1	s__Terricaulis sp017303355	78.8499	104	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791365.1	s__Terricaulis sp016791365	78.7962	119	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242075.1	s__Terricaulis sp003242075	78.6644	113	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004634425.1	s__Terricaulis sp004634425	78.6349	97	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378995.1	s__Terricaulis sp014378995	78.3634	101	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791325.1	s__Terricaulis sp016791325	78.1776	56	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000974665.1	s__Terricaulis sp000974665	78.1462	67	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001679665.1	s__Terricaulis sp001679665	78.1186	107	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:36:23,554] [INFO] GTDB search result was written to OceanDNA-b23832/result_gtdb.tsv
[2023-03-18 01:36:23,555] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:36:23,557] [INFO] DFAST_QC result json was written to OceanDNA-b23832/dqc_result.json
[2023-03-18 01:36:23,557] [INFO] DFAST_QC completed!
[2023-03-18 01:36:23,557] [INFO] Total running time: 0h1m7s