[2023-03-18 01:26:26,320] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,320] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference
[2023-03-18 01:26:27,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,458] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,459] [INFO] Running command: cat /var/lib/cwl/stg0878c582-1006-4cb0-b228-59f0ae390247/OceanDNA-b32551.fa | prodigal -d OceanDNA-b32551/cds.fna -a OceanDNA-b32551/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:32,819] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:32,819] [INFO] Task started: HMMsearch
[2023-03-18 01:26:32,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b32551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference/reference_markers.hmm OceanDNA-b32551/protein.faa > /dev/null
[2023-03-18 01:26:32,981] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:32,981] [INFO] Found 6/6 markers.
[2023-03-18 01:26:32,990] [INFO] Query marker FASTA was written to OceanDNA-b32551/markers.fasta
[2023-03-18 01:26:32,990] [INFO] Task started: Blastn
[2023-03-18 01:26:32,990] [INFO] Running command: blastn -query OceanDNA-b32551/markers.fasta -db /var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference/reference_markers.fasta -out OceanDNA-b32551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:33,515] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:33,516] [INFO] Selected 16 target genomes.
[2023-03-18 01:26:33,516] [INFO] Target genome list was writen to OceanDNA-b32551/target_genomes.txt
[2023-03-18 01:26:33,528] [INFO] Task started: fastANI
[2023-03-18 01:26:33,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg0878c582-1006-4cb0-b228-59f0ae390247/OceanDNA-b32551.fa --refList OceanDNA-b32551/target_genomes.txt --output OceanDNA-b32551/fastani_result.tsv --threads 1
[2023-03-18 01:26:39,579] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:39,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:39,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:39,579] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:39,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:39,580] [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 01:26:39,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32551/tc_result.tsv
[2023-03-18 01:26:39,580] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:39,580] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:39,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference/checkm_data
[2023-03-18 01:26:39,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:39,586] [INFO] Task started: CheckM
[2023-03-18 01:26:39,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32551/checkm_input OceanDNA-b32551/checkm_result
[2023-03-18 01:26:59,116] [INFO] Task succeeded: CheckM
[2023-03-18 01:26:59,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:26:59,121] [INFO] ===== Completeness check finished =====
[2023-03-18 01:26:59,121] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:26:59,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32551/markers.fasta)
[2023-03-18 01:26:59,121] [INFO] Task started: Blastn
[2023-03-18 01:26:59,121] [INFO] Running command: blastn -query OceanDNA-b32551/markers.fasta -db /var/lib/cwl/stg4d994fda-d519-4703-9a5d-4baa64f45222/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:59,892] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:59,893] [INFO] Selected 26 target genomes.
[2023-03-18 01:26:59,893] [INFO] Target genome list was writen to OceanDNA-b32551/target_genomes_gtdb.txt
[2023-03-18 01:26:59,918] [INFO] Task started: fastANI
[2023-03-18 01:26:59,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg0878c582-1006-4cb0-b228-59f0ae390247/OceanDNA-b32551.fa --refList OceanDNA-b32551/target_genomes_gtdb.txt --output OceanDNA-b32551/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:06,354] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:06,360] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:27:06,360] [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_002457065.1	s__MED-G10 sp002457065	99.4093	249	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.75	96.52	0.68	0.65	3	conclusive
GCA_902547955.1	s__MED-G10 sp902547955	78.084	143	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.61	97.06	0.82	0.80	5	-
GCA_002712255.1	s__MED-G10 sp002712255	77.7915	137	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618535.1	s__GCA-002690875 sp902618535	76.3607	74	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	97.44	97.44	0.66	0.66	2	-
GCA_902537615.1	s__GCA-002690875 sp902537615	76.2941	70	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	96.75	96.75	0.77	0.77	2	-
GCA_902613995.1	s__GCA-2691245 sp902613995	76.1671	65	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526865.1	s__GCA-2691245 sp902526865	76.0036	54	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690875.1	s__GCA-002690875 sp002690875	75.7837	68	345	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:06,361] [INFO] GTDB search result was written to OceanDNA-b32551/result_gtdb.tsv
[2023-03-18 01:27:06,361] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:06,362] [INFO] DFAST_QC result json was written to OceanDNA-b32551/dqc_result.json
[2023-03-18 01:27:06,362] [INFO] DFAST_QC completed!
[2023-03-18 01:27:06,362] [INFO] Total running time: 0h0m40s