[2023-03-17 13:01:51,489] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,489] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,489] [INFO] DQC Reference Directory: /var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference
[2023-03-17 13:01:52,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,665] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,665] [INFO] Running command: cat /var/lib/cwl/stg31ab0e5a-516d-4e68-90b9-5aa2c6c034d8/OceanDNA-b11599.fa | prodigal -d OceanDNA-b11599/cds.fna -a OceanDNA-b11599/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:00,149] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:00,149] [INFO] Task started: HMMsearch
[2023-03-17 13:02:00,149] [INFO] Running command: hmmsearch --tblout OceanDNA-b11599/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference/reference_markers.hmm OceanDNA-b11599/protein.faa > /dev/null
[2023-03-17 13:02:00,343] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:00,344] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg31ab0e5a-516d-4e68-90b9-5aa2c6c034d8/OceanDNA-b11599.fa]
[2023-03-17 13:02:00,353] [INFO] Query marker FASTA was written to OceanDNA-b11599/markers.fasta
[2023-03-17 13:02:00,353] [INFO] Task started: Blastn
[2023-03-17 13:02:00,353] [INFO] Running command: blastn -query OceanDNA-b11599/markers.fasta -db /var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference/reference_markers.fasta -out OceanDNA-b11599/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:00,913] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:00,913] [INFO] Selected 25 target genomes.
[2023-03-17 13:02:00,914] [INFO] Target genome list was writen to OceanDNA-b11599/target_genomes.txt
[2023-03-17 13:02:00,925] [INFO] Task started: fastANI
[2023-03-17 13:02:00,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ab0e5a-516d-4e68-90b9-5aa2c6c034d8/OceanDNA-b11599.fa --refList OceanDNA-b11599/target_genomes.txt --output OceanDNA-b11599/fastani_result.tsv --threads 1
[2023-03-17 13:02:15,493] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:15,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:15,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:15,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:15,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:15,493] [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 13:02:15,494] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11599/tc_result.tsv
[2023-03-17 13:02:15,494] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:15,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:15,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference/checkm_data
[2023-03-17 13:02:15,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:15,500] [INFO] Task started: CheckM
[2023-03-17 13:02:15,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11599/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11599/checkm_input OceanDNA-b11599/checkm_result
[2023-03-17 13:02:39,329] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:39,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:39,330] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:39,331] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:39,331] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11599/markers.fasta)
[2023-03-17 13:02:39,331] [INFO] Task started: Blastn
[2023-03-17 13:02:39,331] [INFO] Running command: blastn -query OceanDNA-b11599/markers.fasta -db /var/lib/cwl/stga2fc8bb9-4539-46c7-af7c-64699323ee7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11599/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:40,220] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:40,221] [INFO] Selected 22 target genomes.
[2023-03-17 13:02:40,221] [INFO] Target genome list was writen to OceanDNA-b11599/target_genomes_gtdb.txt
[2023-03-17 13:02:40,666] [INFO] Task started: fastANI
[2023-03-17 13:02:40,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ab0e5a-516d-4e68-90b9-5aa2c6c034d8/OceanDNA-b11599.fa --refList OceanDNA-b11599/target_genomes_gtdb.txt --output OceanDNA-b11599/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:46,427] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:46,431] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:02:46,431] [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_002718035.1	s__GCA-2718035 sp002718035	99.3982	366	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902520385.1	s__GCA-2718035 sp902520385	78.7735	117	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533035.1	s__GCA-2718035 sp902533035	77.9808	153	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718035	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713285.1	s__SP256 sp002713285	75.8597	55	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	75.6246	50	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:46,431] [INFO] GTDB search result was written to OceanDNA-b11599/result_gtdb.tsv
[2023-03-17 13:02:46,431] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:46,432] [INFO] DFAST_QC result json was written to OceanDNA-b11599/dqc_result.json
[2023-03-17 13:02:46,432] [INFO] DFAST_QC completed!
[2023-03-17 13:02:46,432] [INFO] Total running time: 0h0m55s