[2023-03-15 03:14:16,432] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference
[2023-03-15 03:14:17,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,735] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,736] [INFO] Running command: cat /var/lib/cwl/stg07c9b454-e459-466a-82b4-b2172fa3ae0d/OceanDNA-b37750.fa | prodigal -d OceanDNA-b37750/cds.fna -a OceanDNA-b37750/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:24,007] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:24,007] [INFO] Task started: HMMsearch
[2023-03-15 03:14:24,007] [INFO] Running command: hmmsearch --tblout OceanDNA-b37750/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference/reference_markers.hmm OceanDNA-b37750/protein.faa > /dev/null
[2023-03-15 03:14:24,201] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:24,201] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg07c9b454-e459-466a-82b4-b2172fa3ae0d/OceanDNA-b37750.fa]
[2023-03-15 03:14:24,214] [INFO] Query marker FASTA was written to OceanDNA-b37750/markers.fasta
[2023-03-15 03:14:24,214] [INFO] Task started: Blastn
[2023-03-15 03:14:24,214] [INFO] Running command: blastn -query OceanDNA-b37750/markers.fasta -db /var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference/reference_markers.fasta -out OceanDNA-b37750/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:24,758] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:24,758] [INFO] Selected 22 target genomes.
[2023-03-15 03:14:24,759] [INFO] Target genome list was writen to OceanDNA-b37750/target_genomes.txt
[2023-03-15 03:14:24,796] [INFO] Task started: fastANI
[2023-03-15 03:14:24,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg07c9b454-e459-466a-82b4-b2172fa3ae0d/OceanDNA-b37750.fa --refList OceanDNA-b37750/target_genomes.txt --output OceanDNA-b37750/fastani_result.tsv --threads 1
[2023-03-15 03:14:38,969] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:38,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:38,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:38,970] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:38,970] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:14:38,970] [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
--------------------------------------------------------------------------------
[2023-03-15 03:14:38,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37750/tc_result.tsv
[2023-03-15 03:14:38,970] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:38,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:38,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference/checkm_data
[2023-03-15 03:14:38,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:38,977] [INFO] Task started: CheckM
[2023-03-15 03:14:38,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37750/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37750/checkm_input OceanDNA-b37750/checkm_result
[2023-03-15 03:15:00,854] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:00,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:00,878] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:00,879] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:00,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37750/markers.fasta)
[2023-03-15 03:15:00,879] [INFO] Task started: Blastn
[2023-03-15 03:15:00,879] [INFO] Running command: blastn -query OceanDNA-b37750/markers.fasta -db /var/lib/cwl/stg37f3eb49-aa09-4117-b945-89dd0f7196c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37750/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:01,565] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:01,565] [INFO] Selected 12 target genomes.
[2023-03-15 03:15:01,565] [INFO] Target genome list was writen to OceanDNA-b37750/target_genomes_gtdb.txt
[2023-03-15 03:15:01,574] [INFO] Task started: fastANI
[2023-03-15 03:15:01,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg07c9b454-e459-466a-82b4-b2172fa3ae0d/OceanDNA-b37750.fa --refList OceanDNA-b37750/target_genomes_gtdb.txt --output OceanDNA-b37750/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:05,577] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:05,583] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:05,583] [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_902623175.1	s__Luminiphilus sp902623175	94.4212	208	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518075.1	s__Luminiphilus sp902518075	89.0968	124	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520195.1	s__Luminiphilus sp902520195	87.4645	164	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_018222695.1	s__Luminiphilus sp018222695	84.2286	170	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	83.8264	162	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331685.1	s__Luminiphilus sp003331685	83.1852	114	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778045.1	s__Luminiphilus sp016778045	80.3456	74	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721785.1	s__Luminiphilus sp002721785	78.0457	88	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002377985.1	s__Luminiphilus sp002377985	77.4707	51	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:05,583] [INFO] GTDB search result was written to OceanDNA-b37750/result_gtdb.tsv
[2023-03-15 03:15:05,583] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:05,584] [INFO] DFAST_QC result json was written to OceanDNA-b37750/dqc_result.json
[2023-03-15 03:15:05,584] [INFO] DFAST_QC completed!
[2023-03-15 03:15:05,584] [INFO] Total running time: 0h0m49s