[2023-06-18 12:30:58,067] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:30:58,069] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:30:58,070] [INFO] DQC Reference Directory: /var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference
[2023-06-18 12:30:59,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:30:59,371] [INFO] Task started: Prodigal
[2023-06-18 12:30:59,373] [INFO] Running command: gunzip -c /var/lib/cwl/stg93e968b7-b6f8-4f75-80e2-677b7a8c4382/GCA_018698535.1_ASM1869853v1_genomic.fna.gz | prodigal -d GCA_018698535.1_ASM1869853v1_genomic.fna/cds.fna -a GCA_018698535.1_ASM1869853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:31:03,211] [INFO] Task succeeded: Prodigal
[2023-06-18 12:31:03,212] [INFO] Task started: HMMsearch
[2023-06-18 12:31:03,212] [INFO] Running command: hmmsearch --tblout GCA_018698535.1_ASM1869853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference/reference_markers.hmm GCA_018698535.1_ASM1869853v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:31:03,449] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:31:03,451] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg93e968b7-b6f8-4f75-80e2-677b7a8c4382/GCA_018698535.1_ASM1869853v1_genomic.fna.gz]
[2023-06-18 12:31:03,484] [INFO] Query marker FASTA was written to GCA_018698535.1_ASM1869853v1_genomic.fna/markers.fasta
[2023-06-18 12:31:03,484] [INFO] Task started: Blastn
[2023-06-18 12:31:03,484] [INFO] Running command: blastn -query GCA_018698535.1_ASM1869853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference/reference_markers.fasta -out GCA_018698535.1_ASM1869853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:04,087] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:04,091] [INFO] Selected 23 target genomes.
[2023-06-18 12:31:04,091] [INFO] Target genome list was writen to GCA_018698535.1_ASM1869853v1_genomic.fna/target_genomes.txt
[2023-06-18 12:31:04,098] [INFO] Task started: fastANI
[2023-06-18 12:31:04,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e968b7-b6f8-4f75-80e2-677b7a8c4382/GCA_018698535.1_ASM1869853v1_genomic.fna.gz --refList GCA_018698535.1_ASM1869853v1_genomic.fna/target_genomes.txt --output GCA_018698535.1_ASM1869853v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:31:15,237] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:15,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:31:15,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:31:15,239] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:31:15,239] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:31:15,239] [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
--------------------------------------------------------------------------------
[2023-06-18 12:31:15,241] [INFO] DFAST Taxonomy check result was written to GCA_018698535.1_ASM1869853v1_genomic.fna/tc_result.tsv
[2023-06-18 12:31:15,242] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:31:15,242] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:31:15,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference/checkm_data
[2023-06-18 12:31:15,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:31:15,273] [INFO] Task started: CheckM
[2023-06-18 12:31:15,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018698535.1_ASM1869853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018698535.1_ASM1869853v1_genomic.fna/checkm_input GCA_018698535.1_ASM1869853v1_genomic.fna/checkm_result
[2023-06-18 12:31:34,543] [INFO] Task succeeded: CheckM
[2023-06-18 12:31:34,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:31:34,575] [INFO] ===== Completeness check finished =====
[2023-06-18 12:31:34,575] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:31:34,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018698535.1_ASM1869853v1_genomic.fna/markers.fasta)
[2023-06-18 12:31:34,576] [INFO] Task started: Blastn
[2023-06-18 12:31:34,576] [INFO] Running command: blastn -query GCA_018698535.1_ASM1869853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc620f4d3-92d6-4a70-b2c7-77c3762fd5ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_018698535.1_ASM1869853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:35,518] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:35,527] [INFO] Selected 18 target genomes.
[2023-06-18 12:31:35,528] [INFO] Target genome list was writen to GCA_018698535.1_ASM1869853v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:31:35,565] [INFO] Task started: fastANI
[2023-06-18 12:31:35,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e968b7-b6f8-4f75-80e2-677b7a8c4382/GCA_018698535.1_ASM1869853v1_genomic.fna.gz --refList GCA_018698535.1_ASM1869853v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018698535.1_ASM1869853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:31:41,336] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:41,346] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:31:41,346] [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_905478365.1	s__UBA3031 sp905478365	98.4838	398	521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	98.56	98.18	0.78	0.69	7	conclusive
GCA_002167745.1	s__UBA3031 sp002167745	80.5161	305	521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	99.76	99.76	0.94	0.94	2	-
GCA_009886305.1	s__UBA3031 sp009886305	80.4799	254	521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367635.1	s__UBA3031 sp002367635	76.9305	80	521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	99.64	99.62	0.86	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-18 12:31:41,348] [INFO] GTDB search result was written to GCA_018698535.1_ASM1869853v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:31:41,351] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:31:41,354] [INFO] DFAST_QC result json was written to GCA_018698535.1_ASM1869853v1_genomic.fna/dqc_result.json
[2023-06-18 12:31:41,354] [INFO] DFAST_QC completed!
[2023-06-18 12:31:41,354] [INFO] Total running time: 0h0m43s