[2023-03-16 18:18:12,619] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference
[2023-03-16 18:18:13,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,706] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,706] [INFO] Running command: cat /var/lib/cwl/stg7b26d0cc-9d59-4d2a-b85a-2159822f0337/OceanDNA-b45526.fa | prodigal -d OceanDNA-b45526/cds.fna -a OceanDNA-b45526/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:24,764] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:24,765] [INFO] Task started: HMMsearch
[2023-03-16 18:18:24,765] [INFO] Running command: hmmsearch --tblout OceanDNA-b45526/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference/reference_markers.hmm OceanDNA-b45526/protein.faa > /dev/null
[2023-03-16 18:18:24,934] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:24,934] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7b26d0cc-9d59-4d2a-b85a-2159822f0337/OceanDNA-b45526.fa]
[2023-03-16 18:18:24,944] [INFO] Query marker FASTA was written to OceanDNA-b45526/markers.fasta
[2023-03-16 18:18:24,945] [INFO] Task started: Blastn
[2023-03-16 18:18:24,945] [INFO] Running command: blastn -query OceanDNA-b45526/markers.fasta -db /var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference/reference_markers.fasta -out OceanDNA-b45526/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:25,404] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:25,404] [INFO] Selected 7 target genomes.
[2023-03-16 18:18:25,405] [INFO] Target genome list was writen to OceanDNA-b45526/target_genomes.txt
[2023-03-16 18:18:25,427] [INFO] Task started: fastANI
[2023-03-16 18:18:25,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b26d0cc-9d59-4d2a-b85a-2159822f0337/OceanDNA-b45526.fa --refList OceanDNA-b45526/target_genomes.txt --output OceanDNA-b45526/fastani_result.tsv --threads 1
[2023-03-16 18:18:29,015] [INFO] Task succeeded: fastANI
[2023-03-16 18:18:29,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:18:29,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:18:29,016] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:18:29,016] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:18:29,016] [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
--------------------------------------------------------------------------------
[2023-03-16 18:18:29,016] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45526/tc_result.tsv
[2023-03-16 18:18:29,017] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:18:29,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:18:29,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference/checkm_data
[2023-03-16 18:18:29,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:18:29,077] [INFO] Task started: CheckM
[2023-03-16 18:18:29,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45526/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45526/checkm_input OceanDNA-b45526/checkm_result
[2023-03-16 18:19:02,122] [INFO] Task succeeded: CheckM
[2023-03-16 18:19:02,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:19:02,124] [INFO] ===== Completeness check finished =====
[2023-03-16 18:19:02,124] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:19:02,124] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45526/markers.fasta)
[2023-03-16 18:19:02,124] [INFO] Task started: Blastn
[2023-03-16 18:19:02,124] [INFO] Running command: blastn -query OceanDNA-b45526/markers.fasta -db /var/lib/cwl/stg69dc0827-8231-49e1-bb2c-88c258277d38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45526/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:19:02,532] [INFO] Task succeeded: Blastn
[2023-03-16 18:19:02,533] [INFO] Selected 11 target genomes.
[2023-03-16 18:19:02,533] [INFO] Target genome list was writen to OceanDNA-b45526/target_genomes_gtdb.txt
[2023-03-16 18:19:02,663] [INFO] Task started: fastANI
[2023-03-16 18:19:02,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b26d0cc-9d59-4d2a-b85a-2159822f0337/OceanDNA-b45526.fa --refList OceanDNA-b45526/target_genomes_gtdb.txt --output OceanDNA-b45526/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:19:05,792] [INFO] Task succeeded: fastANI
[2023-03-16 18:19:05,794] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:19:05,794] [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_018607205.1	s__MB11C04 sp018607205	79.3113	84	312	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.05	99.05	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:19:05,794] [INFO] GTDB search result was written to OceanDNA-b45526/result_gtdb.tsv
[2023-03-16 18:19:05,794] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:19:05,795] [INFO] DFAST_QC result json was written to OceanDNA-b45526/dqc_result.json
[2023-03-16 18:19:05,795] [INFO] DFAST_QC completed!
[2023-03-16 18:19:05,795] [INFO] Total running time: 0h0m53s