[2023-06-30 06:59:08,913] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:59:08,916] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:59:08,916] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference
[2023-06-30 06:59:11,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:59:11,268] [INFO] Task started: Prodigal
[2023-06-30 06:59:11,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg46c8d0c2-f166-41e0-86aa-92d45cb33f74/GCA_024960045.1_ASM2496004v1_genomic.fna.gz | prodigal -d GCA_024960045.1_ASM2496004v1_genomic.fna/cds.fna -a GCA_024960045.1_ASM2496004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:59:16,967] [INFO] Task succeeded: Prodigal
[2023-06-30 06:59:16,968] [INFO] Task started: HMMsearch
[2023-06-30 06:59:16,968] [INFO] Running command: hmmsearch --tblout GCA_024960045.1_ASM2496004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference/reference_markers.hmm GCA_024960045.1_ASM2496004v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:59:17,161] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:59:17,163] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg46c8d0c2-f166-41e0-86aa-92d45cb33f74/GCA_024960045.1_ASM2496004v1_genomic.fna.gz]
[2023-06-30 06:59:17,182] [INFO] Query marker FASTA was written to GCA_024960045.1_ASM2496004v1_genomic.fna/markers.fasta
[2023-06-30 06:59:17,183] [INFO] Task started: Blastn
[2023-06-30 06:59:17,183] [INFO] Running command: blastn -query GCA_024960045.1_ASM2496004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference/reference_markers.fasta -out GCA_024960045.1_ASM2496004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:59:17,653] [INFO] Task succeeded: Blastn
[2023-06-30 06:59:17,657] [INFO] Selected 5 target genomes.
[2023-06-30 06:59:17,657] [INFO] Target genome list was writen to GCA_024960045.1_ASM2496004v1_genomic.fna/target_genomes.txt
[2023-06-30 06:59:17,660] [INFO] Task started: fastANI
[2023-06-30 06:59:17,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c8d0c2-f166-41e0-86aa-92d45cb33f74/GCA_024960045.1_ASM2496004v1_genomic.fna.gz --refList GCA_024960045.1_ASM2496004v1_genomic.fna/target_genomes.txt --output GCA_024960045.1_ASM2496004v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:59:20,151] [INFO] Task succeeded: fastANI
[2023-06-30 06:59:20,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:59:20,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:59:20,155] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:59:20,155] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:59:20,155] [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 06:59:20,157] [INFO] DFAST Taxonomy check result was written to GCA_024960045.1_ASM2496004v1_genomic.fna/tc_result.tsv
[2023-06-30 06:59:20,158] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:59:20,158] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:59:20,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference/checkm_data
[2023-06-30 06:59:20,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:59:20,183] [INFO] Task started: CheckM
[2023-06-30 06:59:20,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024960045.1_ASM2496004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024960045.1_ASM2496004v1_genomic.fna/checkm_input GCA_024960045.1_ASM2496004v1_genomic.fna/checkm_result
[2023-06-30 06:59:43,392] [INFO] Task succeeded: CheckM
[2023-06-30 06:59:43,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.33%
Contamintation: 1.36%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 06:59:43,414] [INFO] ===== Completeness check finished =====
[2023-06-30 06:59:43,415] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:59:43,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024960045.1_ASM2496004v1_genomic.fna/markers.fasta)
[2023-06-30 06:59:43,415] [INFO] Task started: Blastn
[2023-06-30 06:59:43,416] [INFO] Running command: blastn -query GCA_024960045.1_ASM2496004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc747b9-338d-43c0-8615-e3dfd372ae61/dqc_reference/reference_markers_gtdb.fasta -out GCA_024960045.1_ASM2496004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:59:43,853] [INFO] Task succeeded: Blastn
[2023-06-30 06:59:43,857] [INFO] Selected 11 target genomes.
[2023-06-30 06:59:43,857] [INFO] Target genome list was writen to GCA_024960045.1_ASM2496004v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:59:43,866] [INFO] Task started: fastANI
[2023-06-30 06:59:43,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c8d0c2-f166-41e0-86aa-92d45cb33f74/GCA_024960045.1_ASM2496004v1_genomic.fna.gz --refList GCA_024960045.1_ASM2496004v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024960045.1_ASM2496004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:59:46,303] [INFO] Task succeeded: fastANI
[2023-06-30 06:59:46,312] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:59:46,312] [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_004195715.1	s__Thalassarchaeum sp004195715	80.2964	74	101	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	80.1153	71	101	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495735.1	s__Thalassarchaeum sp002495735	79.8197	65	101	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505325.1	s__Thalassarchaeum sp002505325	79.5847	67	101	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:59:46,314] [INFO] GTDB search result was written to GCA_024960045.1_ASM2496004v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:59:46,315] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:59:46,318] [INFO] DFAST_QC result json was written to GCA_024960045.1_ASM2496004v1_genomic.fna/dqc_result.json
[2023-06-30 06:59:46,318] [INFO] DFAST_QC completed!
[2023-06-30 06:59:46,319] [INFO] Total running time: 0h0m37s