[2023-03-17 23:43:20,546] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:43:20,548] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:43:20,548] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference
[2023-03-17 23:43:21,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:43:21,650] [INFO] Task started: Prodigal
[2023-03-17 23:43:21,650] [INFO] Running command: cat /var/lib/cwl/stg7c344785-f77c-4b4a-8f95-d8fdbae5b5e6/OceanDNA-b10476.fa | prodigal -d OceanDNA-b10476/cds.fna -a OceanDNA-b10476/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:43:31,043] [INFO] Task succeeded: Prodigal
[2023-03-17 23:43:31,044] [INFO] Task started: HMMsearch
[2023-03-17 23:43:31,044] [INFO] Running command: hmmsearch --tblout OceanDNA-b10476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference/reference_markers.hmm OceanDNA-b10476/protein.faa > /dev/null
[2023-03-17 23:43:31,206] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:43:31,206] [INFO] Found 6/6 markers.
[2023-03-17 23:43:31,217] [INFO] Query marker FASTA was written to OceanDNA-b10476/markers.fasta
[2023-03-17 23:43:31,218] [INFO] Task started: Blastn
[2023-03-17 23:43:31,218] [INFO] Running command: blastn -query OceanDNA-b10476/markers.fasta -db /var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference/reference_markers.fasta -out OceanDNA-b10476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:31,805] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:31,807] [INFO] Selected 27 target genomes.
[2023-03-17 23:43:31,808] [INFO] Target genome list was writen to OceanDNA-b10476/target_genomes.txt
[2023-03-17 23:43:31,900] [INFO] Task started: fastANI
[2023-03-17 23:43:31,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c344785-f77c-4b4a-8f95-d8fdbae5b5e6/OceanDNA-b10476.fa --refList OceanDNA-b10476/target_genomes.txt --output OceanDNA-b10476/fastani_result.tsv --threads 1
[2023-03-17 23:43:49,013] [INFO] Task succeeded: fastANI
[2023-03-17 23:43:49,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:43:49,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:43:49,015] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:43:49,015] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:43:49,015] [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 23:43:49,015] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10476/tc_result.tsv
[2023-03-17 23:43:49,015] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:43:49,015] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:43:49,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference/checkm_data
[2023-03-17 23:43:49,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:43:49,026] [INFO] Task started: CheckM
[2023-03-17 23:43:49,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10476/checkm_input OceanDNA-b10476/checkm_result
[2023-03-17 23:44:17,952] [INFO] Task succeeded: CheckM
[2023-03-17 23:44:17,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.43%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:44:17,959] [INFO] ===== Completeness check finished =====
[2023-03-17 23:44:17,959] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:44:17,959] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10476/markers.fasta)
[2023-03-17 23:44:17,960] [INFO] Task started: Blastn
[2023-03-17 23:44:17,960] [INFO] Running command: blastn -query OceanDNA-b10476/markers.fasta -db /var/lib/cwl/stgcf3c2526-3b0e-498b-b02f-148910e1ed23/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:44:18,927] [INFO] Task succeeded: Blastn
[2023-03-17 23:44:18,928] [INFO] Selected 26 target genomes.
[2023-03-17 23:44:18,928] [INFO] Target genome list was writen to OceanDNA-b10476/target_genomes_gtdb.txt
[2023-03-17 23:44:18,951] [INFO] Task started: fastANI
[2023-03-17 23:44:18,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c344785-f77c-4b4a-8f95-d8fdbae5b5e6/OceanDNA-b10476.fa --refList OceanDNA-b10476/target_genomes_gtdb.txt --output OceanDNA-b10476/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:44:28,538] [INFO] Task succeeded: fastANI
[2023-03-17 23:44:28,541] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:44:28,541] [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_009886755.1	s__UBA11891 sp009886755	87.1556	311	349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	99.16	98.70	0.90	0.89	3	-
GCA_011524905.1	s__UBA11891 sp011524905	77.2223	85	349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533785.1	s__UBA11891 sp003533785	77.2199	78	349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA11891	95.0	99.52	99.52	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:44:28,541] [INFO] GTDB search result was written to OceanDNA-b10476/result_gtdb.tsv
[2023-03-17 23:44:28,542] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:44:28,542] [INFO] DFAST_QC result json was written to OceanDNA-b10476/dqc_result.json
[2023-03-17 23:44:28,542] [INFO] DFAST_QC completed!
[2023-03-17 23:44:28,542] [INFO] Total running time: 0h1m8s