[2023-03-17 10:48:45,655] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,655] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference
[2023-03-17 10:48:46,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,774] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,774] [INFO] Running command: cat /var/lib/cwl/stg297d01b3-d2a3-4e3b-ac15-c7b64bf741ac/OceanDNA-a4763.fa | prodigal -d OceanDNA-a4763/cds.fna -a OceanDNA-a4763/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:51,119] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:51,119] [INFO] Task started: HMMsearch
[2023-03-17 10:48:51,119] [INFO] Running command: hmmsearch --tblout OceanDNA-a4763/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference/reference_markers.hmm OceanDNA-a4763/protein.faa > /dev/null
[2023-03-17 10:48:51,305] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:51,305] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg297d01b3-d2a3-4e3b-ac15-c7b64bf741ac/OceanDNA-a4763.fa]
[2023-03-17 10:48:51,316] [INFO] Query marker FASTA was written to OceanDNA-a4763/markers.fasta
[2023-03-17 10:48:51,316] [INFO] Task started: Blastn
[2023-03-17 10:48:51,316] [INFO] Running command: blastn -query OceanDNA-a4763/markers.fasta -db /var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference/reference_markers.fasta -out OceanDNA-a4763/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:51,840] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:51,841] [INFO] Selected 4 target genomes.
[2023-03-17 10:48:51,842] [INFO] Target genome list was writen to OceanDNA-a4763/target_genomes.txt
[2023-03-17 10:48:51,845] [INFO] Task started: fastANI
[2023-03-17 10:48:51,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg297d01b3-d2a3-4e3b-ac15-c7b64bf741ac/OceanDNA-a4763.fa --refList OceanDNA-a4763/target_genomes.txt --output OceanDNA-a4763/fastani_result.tsv --threads 1
[2023-03-17 10:48:54,390] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:54,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:54,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:54,390] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:54,391] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:54,391] [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
--------------------------------------------------------------------------------
[2023-03-17 10:48:54,391] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4763/tc_result.tsv
[2023-03-17 10:48:54,391] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:54,391] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:54,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference/checkm_data
[2023-03-17 10:48:54,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:54,912] [INFO] Task started: CheckM
[2023-03-17 10:48:54,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4763/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4763/checkm_input OceanDNA-a4763/checkm_result
[2023-03-17 10:49:13,555] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:13,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.13%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:13,558] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:13,558] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:13,559] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4763/markers.fasta)
[2023-03-17 10:49:13,559] [INFO] Task started: Blastn
[2023-03-17 10:49:13,559] [INFO] Running command: blastn -query OceanDNA-a4763/markers.fasta -db /var/lib/cwl/stg92a4902b-c8b0-4a35-b55b-73f19d871219/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4763/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:14,288] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:14,289] [INFO] Selected 14 target genomes.
[2023-03-17 10:49:14,289] [INFO] Target genome list was writen to OceanDNA-a4763/target_genomes_gtdb.txt
[2023-03-17 10:49:14,707] [INFO] Task started: fastANI
[2023-03-17 10:49:14,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg297d01b3-d2a3-4e3b-ac15-c7b64bf741ac/OceanDNA-a4763.fa --refList OceanDNA-a4763/target_genomes_gtdb.txt --output OceanDNA-a4763/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:18,749] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:18,751] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:49:18,752] [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_002498455.1	s__MGIIb-P sp002498455	77.6343	51	156	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	98.13	97.46	0.87	0.81	6	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:18,752] [INFO] GTDB search result was written to OceanDNA-a4763/result_gtdb.tsv
[2023-03-17 10:49:18,752] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:18,753] [INFO] DFAST_QC result json was written to OceanDNA-a4763/dqc_result.json
[2023-03-17 10:49:18,753] [INFO] DFAST_QC completed!
[2023-03-17 10:49:18,753] [INFO] Total running time: 0h0m33s