[2023-03-17 22:37:12,599] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference
[2023-03-17 22:37:14,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,350] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,350] [INFO] Running command: cat /var/lib/cwl/stg54fadb49-8cc1-4ea6-a5e7-79fb01aad63c/OceanDNA-b45647.fa | prodigal -d OceanDNA-b45647/cds.fna -a OceanDNA-b45647/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:23,698] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:23,699] [INFO] Task started: HMMsearch
[2023-03-17 22:37:23,699] [INFO] Running command: hmmsearch --tblout OceanDNA-b45647/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference/reference_markers.hmm OceanDNA-b45647/protein.faa > /dev/null
[2023-03-17 22:37:23,863] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:23,863] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg54fadb49-8cc1-4ea6-a5e7-79fb01aad63c/OceanDNA-b45647.fa]
[2023-03-17 22:37:23,878] [INFO] Query marker FASTA was written to OceanDNA-b45647/markers.fasta
[2023-03-17 22:37:23,879] [INFO] Task started: Blastn
[2023-03-17 22:37:23,879] [INFO] Running command: blastn -query OceanDNA-b45647/markers.fasta -db /var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference/reference_markers.fasta -out OceanDNA-b45647/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:24,310] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:24,311] [INFO] Selected 9 target genomes.
[2023-03-17 22:37:24,311] [INFO] Target genome list was writen to OceanDNA-b45647/target_genomes.txt
[2023-03-17 22:37:24,315] [INFO] Task started: fastANI
[2023-03-17 22:37:24,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg54fadb49-8cc1-4ea6-a5e7-79fb01aad63c/OceanDNA-b45647.fa --refList OceanDNA-b45647/target_genomes.txt --output OceanDNA-b45647/fastani_result.tsv --threads 1
[2023-03-17 22:37:29,211] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:29,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:29,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:29,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:29,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:37:29,212] [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 22:37:29,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45647/tc_result.tsv
[2023-03-17 22:37:29,213] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:29,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:29,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference/checkm_data
[2023-03-17 22:37:29,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:29,224] [INFO] Task started: CheckM
[2023-03-17 22:37:29,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45647/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45647/checkm_input OceanDNA-b45647/checkm_result
[2023-03-17 22:37:58,942] [INFO] Task succeeded: CheckM
[2023-03-17 22:37:58,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.32%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 22:37:58,945] [INFO] ===== Completeness check finished =====
[2023-03-17 22:37:58,945] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:37:58,945] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45647/markers.fasta)
[2023-03-17 22:37:58,945] [INFO] Task started: Blastn
[2023-03-17 22:37:58,946] [INFO] Running command: blastn -query OceanDNA-b45647/markers.fasta -db /var/lib/cwl/stg7995a647-9e2d-4e91-9d8f-3ffb655747b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45647/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:59,412] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:59,413] [INFO] Selected 16 target genomes.
[2023-03-17 22:37:59,413] [INFO] Target genome list was writen to OceanDNA-b45647/target_genomes_gtdb.txt
[2023-03-17 22:37:59,530] [INFO] Task started: fastANI
[2023-03-17 22:37:59,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg54fadb49-8cc1-4ea6-a5e7-79fb01aad63c/OceanDNA-b45647.fa --refList OceanDNA-b45647/target_genomes_gtdb.txt --output OceanDNA-b45647/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:38:05,652] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:05,654] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:38:05,655] [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_002171765.1	s__MB11C04 sp002171765	92.5212	106	153	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.33	98.33	0.72	0.72	2	-
GCA_002364975.1	s__MB11C04 sp002364975	90.2446	134	153	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.20	99.18	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 22:38:05,655] [INFO] GTDB search result was written to OceanDNA-b45647/result_gtdb.tsv
[2023-03-17 22:38:05,655] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:38:05,655] [INFO] DFAST_QC result json was written to OceanDNA-b45647/dqc_result.json
[2023-03-17 22:38:05,655] [INFO] DFAST_QC completed!
[2023-03-17 22:38:05,656] [INFO] Total running time: 0h0m53s