[2023-06-30 13:24:11,477] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:11,480] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:11,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference
[2023-06-30 13:24:14,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:14,677] [INFO] Task started: Prodigal
[2023-06-30 13:24:14,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e7f5bc6-8e0a-464d-aed3-d3128c86bf74/GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna.gz | prodigal -d GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/cds.fna -a GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:16,850] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:16,850] [INFO] Task started: HMMsearch
[2023-06-30 13:24:16,850] [INFO] Running command: hmmsearch --tblout GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference/reference_markers.hmm GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:17,074] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:17,076] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1e7f5bc6-8e0a-464d-aed3-d3128c86bf74/GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna.gz]
[2023-06-30 13:24:17,090] [INFO] Query marker FASTA was written to GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/markers.fasta
[2023-06-30 13:24:17,091] [INFO] Task started: Blastn
[2023-06-30 13:24:17,091] [INFO] Running command: blastn -query GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference/reference_markers.fasta -out GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:18,487] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:18,491] [INFO] Selected 18 target genomes.
[2023-06-30 13:24:18,491] [INFO] Target genome list was writen to GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/target_genomes.txt
[2023-06-30 13:24:18,529] [INFO] Task started: fastANI
[2023-06-30 13:24:18,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e7f5bc6-8e0a-464d-aed3-d3128c86bf74/GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna.gz --refList GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/target_genomes.txt --output GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:24:27,977] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:27,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:24:27,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:24:27,979] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:24:27,980] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:24:27,980] [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
--------------------------------------------------------------------------------
[2023-06-30 13:24:27,982] [INFO] DFAST Taxonomy check result was written to GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/tc_result.tsv
[2023-06-30 13:24:27,982] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:24:27,982] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:24:27,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference/checkm_data
[2023-06-30 13:24:27,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:24:28,003] [INFO] Task started: CheckM
[2023-06-30 13:24:28,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/checkm_input GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/checkm_result
[2023-06-30 13:24:43,272] [INFO] Task succeeded: CheckM
[2023-06-30 13:24:43,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 13:24:43,295] [INFO] ===== Completeness check finished =====
[2023-06-30 13:24:43,295] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:24:43,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/markers.fasta)
[2023-06-30 13:24:43,296] [INFO] Task started: Blastn
[2023-06-30 13:24:43,297] [INFO] Running command: blastn -query GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg892e2c47-810b-4e65-933f-3cad9cfd7143/dqc_reference/reference_markers_gtdb.fasta -out GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:44,150] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:44,155] [INFO] Selected 15 target genomes.
[2023-06-30 13:24:44,155] [INFO] Target genome list was writen to GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:24:44,186] [INFO] Task started: fastANI
[2023-06-30 13:24:44,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e7f5bc6-8e0a-464d-aed3-d3128c86bf74/GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna.gz --refList GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:24:49,941] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:49,947] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:24:49,947] [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_000758905.1	s__S5-A14a sp000758905	97.4671	285	316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__S5-A14a	95.0	96.74	96.74	0.81	0.81	2	conclusive
GCA_900553025.1	s__S5-A14a sp900553025	83.0973	217	316	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__S5-A14a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:24:49,949] [INFO] GTDB search result was written to GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 13:24:49,950] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:24:49,952] [INFO] DFAST_QC result json was written to GCA_946221525.1_7PkdMwDRcy_bin.37.MAG_genomic.fna/dqc_result.json
[2023-06-30 13:24:49,952] [INFO] DFAST_QC completed!
[2023-06-30 13:24:49,952] [INFO] Total running time: 0h0m38s