[2023-03-15 21:48:06,733] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,733] [INFO] DQC Reference Directory: /var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference
[2023-03-15 21:48:07,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,852] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,852] [INFO] Running command: cat /var/lib/cwl/stg427fe092-e475-43ca-8df8-04277d35f8e6/OceanDNA-b22674.fa | prodigal -d OceanDNA-b22674/cds.fna -a OceanDNA-b22674/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:17,355] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:17,355] [INFO] Task started: HMMsearch
[2023-03-15 21:48:17,355] [INFO] Running command: hmmsearch --tblout OceanDNA-b22674/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference/reference_markers.hmm OceanDNA-b22674/protein.faa > /dev/null
[2023-03-15 21:48:17,534] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:17,535] [INFO] Found 6/6 markers.
[2023-03-15 21:48:17,552] [INFO] Query marker FASTA was written to OceanDNA-b22674/markers.fasta
[2023-03-15 21:48:17,553] [INFO] Task started: Blastn
[2023-03-15 21:48:17,554] [INFO] Running command: blastn -query OceanDNA-b22674/markers.fasta -db /var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference/reference_markers.fasta -out OceanDNA-b22674/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:18,069] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:18,069] [INFO] Selected 8 target genomes.
[2023-03-15 21:48:18,070] [INFO] Target genome list was writen to OceanDNA-b22674/target_genomes.txt
[2023-03-15 21:48:18,075] [INFO] Task started: fastANI
[2023-03-15 21:48:18,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg427fe092-e475-43ca-8df8-04277d35f8e6/OceanDNA-b22674.fa --refList OceanDNA-b22674/target_genomes.txt --output OceanDNA-b22674/fastani_result.tsv --threads 1
[2023-03-15 21:48:21,435] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:21,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:21,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:21,436] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:21,436] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:21,436] [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 21:48:21,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22674/tc_result.tsv
[2023-03-15 21:48:21,437] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:21,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:21,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference/checkm_data
[2023-03-15 21:48:21,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:21,458] [INFO] Task started: CheckM
[2023-03-15 21:48:21,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22674/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22674/checkm_input OceanDNA-b22674/checkm_result
[2023-03-15 21:48:50,744] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:50,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:50,753] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:50,753] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:50,753] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22674/markers.fasta)
[2023-03-15 21:48:50,754] [INFO] Task started: Blastn
[2023-03-15 21:48:50,755] [INFO] Running command: blastn -query OceanDNA-b22674/markers.fasta -db /var/lib/cwl/stga9b233af-b06d-4a85-92b3-25631c2ba1d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22674/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:51,513] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:51,515] [INFO] Selected 12 target genomes.
[2023-03-15 21:48:51,515] [INFO] Target genome list was writen to OceanDNA-b22674/target_genomes_gtdb.txt
[2023-03-15 21:48:51,532] [INFO] Task started: fastANI
[2023-03-15 21:48:51,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg427fe092-e475-43ca-8df8-04277d35f8e6/OceanDNA-b22674.fa --refList OceanDNA-b22674/target_genomes_gtdb.txt --output OceanDNA-b22674/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:48:57,909] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:57,914] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:48:57,914] [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_002694955.1	s__UBA1268 sp002694955	99.2846	247	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.59	98.49	0.92	0.91	3	conclusive
GCA_003509235.1	s__UBA1268 sp003509235	81.8442	253	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776925.1	s__UBA1268 sp016776925	81.7524	306	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	96.90	0.88	0.85	13	-
GCA_905477565.1	s__UBA1268 sp905477565	81.6925	183	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018694455.1	s__UBA1268 sp018694455	79.0388	146	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	98.58	0.79	0.76	6	-
GCA_002862165.1	s__UBA1268 sp002862165	78.4269	114	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238855.1	s__UBA1268 sp014238855	78.4223	146	395	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:48:57,915] [INFO] GTDB search result was written to OceanDNA-b22674/result_gtdb.tsv
[2023-03-15 21:48:57,921] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:48:57,924] [INFO] DFAST_QC result json was written to OceanDNA-b22674/dqc_result.json
[2023-03-15 21:48:57,924] [INFO] DFAST_QC completed!
[2023-03-15 21:48:57,924] [INFO] Total running time: 0h0m51s