[2023-03-19 01:13:44,406] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,406] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,406] [INFO] DQC Reference Directory: /var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference
[2023-03-19 01:13:45,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,538] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,539] [INFO] Running command: cat /var/lib/cwl/stgbc12c579-0ee2-4102-9eea-adc07212c8a7/OceanDNA-b30776.fa | prodigal -d OceanDNA-b30776/cds.fna -a OceanDNA-b30776/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:54,074] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:54,074] [INFO] Task started: HMMsearch
[2023-03-19 01:13:54,074] [INFO] Running command: hmmsearch --tblout OceanDNA-b30776/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference/reference_markers.hmm OceanDNA-b30776/protein.faa > /dev/null
[2023-03-19 01:13:54,226] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:54,226] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbc12c579-0ee2-4102-9eea-adc07212c8a7/OceanDNA-b30776.fa]
[2023-03-19 01:13:54,241] [INFO] Query marker FASTA was written to OceanDNA-b30776/markers.fasta
[2023-03-19 01:13:54,242] [INFO] Task started: Blastn
[2023-03-19 01:13:54,242] [INFO] Running command: blastn -query OceanDNA-b30776/markers.fasta -db /var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference/reference_markers.fasta -out OceanDNA-b30776/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:54,832] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:54,833] [INFO] Selected 19 target genomes.
[2023-03-19 01:13:54,833] [INFO] Target genome list was writen to OceanDNA-b30776/target_genomes.txt
[2023-03-19 01:13:54,847] [INFO] Task started: fastANI
[2023-03-19 01:13:54,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc12c579-0ee2-4102-9eea-adc07212c8a7/OceanDNA-b30776.fa --refList OceanDNA-b30776/target_genomes.txt --output OceanDNA-b30776/fastani_result.tsv --threads 1
[2023-03-19 01:14:08,481] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:08,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:08,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:08,482] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:08,482] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:14:08,482] [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
--------------------------------------------------------------------------------
[2023-03-19 01:14:08,482] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30776/tc_result.tsv
[2023-03-19 01:14:08,482] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:08,482] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:08,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference/checkm_data
[2023-03-19 01:14:08,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:08,489] [INFO] Task started: CheckM
[2023-03-19 01:14:08,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30776/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30776/checkm_input OceanDNA-b30776/checkm_result
[2023-03-19 01:14:34,590] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:34,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:34,593] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:34,593] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:34,593] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30776/markers.fasta)
[2023-03-19 01:14:34,594] [INFO] Task started: Blastn
[2023-03-19 01:14:34,594] [INFO] Running command: blastn -query OceanDNA-b30776/markers.fasta -db /var/lib/cwl/stge724e714-c99c-42e2-b956-895ce8e8bab0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30776/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:35,491] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:35,491] [INFO] Selected 16 target genomes.
[2023-03-19 01:14:35,492] [INFO] Target genome list was writen to OceanDNA-b30776/target_genomes_gtdb.txt
[2023-03-19 01:14:35,505] [INFO] Task started: fastANI
[2023-03-19 01:14:35,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc12c579-0ee2-4102-9eea-adc07212c8a7/OceanDNA-b30776.fa --refList OceanDNA-b30776/target_genomes_gtdb.txt --output OceanDNA-b30776/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:45,646] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:45,649] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:45,649] [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_018648445.1	s__JABGRG01 sp018648445	82.7608	314	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JABGRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776725.1	s__JABGRG01 sp016776725	82.6706	210	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JABGRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.7892	76	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:45,649] [INFO] GTDB search result was written to OceanDNA-b30776/result_gtdb.tsv
[2023-03-19 01:14:45,650] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:45,650] [INFO] DFAST_QC result json was written to OceanDNA-b30776/dqc_result.json
[2023-03-19 01:14:45,650] [INFO] DFAST_QC completed!
[2023-03-19 01:14:45,650] [INFO] Total running time: 0h1m1s