[2023-06-12 22:53:59,898] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:53:59,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:53:59,900] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference
[2023-06-12 22:54:01,159] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:54:01,160] [INFO] Task started: Prodigal
[2023-06-12 22:54:01,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg368dace9-5f33-4442-9e50-84cfc1524037/GCA_022425205.1_ASM2242520v1_genomic.fna.gz | prodigal -d GCA_022425205.1_ASM2242520v1_genomic.fna/cds.fna -a GCA_022425205.1_ASM2242520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:54:13,684] [INFO] Task succeeded: Prodigal
[2023-06-12 22:54:13,685] [INFO] Task started: HMMsearch
[2023-06-12 22:54:13,685] [INFO] Running command: hmmsearch --tblout GCA_022425205.1_ASM2242520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference/reference_markers.hmm GCA_022425205.1_ASM2242520v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:54:13,945] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:54:13,947] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg368dace9-5f33-4442-9e50-84cfc1524037/GCA_022425205.1_ASM2242520v1_genomic.fna.gz]
[2023-06-12 22:54:13,991] [INFO] Query marker FASTA was written to GCA_022425205.1_ASM2242520v1_genomic.fna/markers.fasta
[2023-06-12 22:54:13,991] [INFO] Task started: Blastn
[2023-06-12 22:54:13,992] [INFO] Running command: blastn -query GCA_022425205.1_ASM2242520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference/reference_markers.fasta -out GCA_022425205.1_ASM2242520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:54:14,564] [INFO] Task succeeded: Blastn
[2023-06-12 22:54:14,569] [INFO] Selected 16 target genomes.
[2023-06-12 22:54:14,570] [INFO] Target genome list was writen to GCA_022425205.1_ASM2242520v1_genomic.fna/target_genomes.txt
[2023-06-12 22:54:14,575] [INFO] Task started: fastANI
[2023-06-12 22:54:14,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg368dace9-5f33-4442-9e50-84cfc1524037/GCA_022425205.1_ASM2242520v1_genomic.fna.gz --refList GCA_022425205.1_ASM2242520v1_genomic.fna/target_genomes.txt --output GCA_022425205.1_ASM2242520v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:54:29,594] [INFO] Task succeeded: fastANI
[2023-06-12 22:54:29,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:54:29,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:54:29,597] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:54:29,598] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-12 22:54:29,598] [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
--------------------------------------------------------------------------------
[2023-06-12 22:54:29,600] [INFO] DFAST Taxonomy check result was written to GCA_022425205.1_ASM2242520v1_genomic.fna/tc_result.tsv
[2023-06-12 22:54:29,601] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:54:29,601] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:54:29,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference/checkm_data
[2023-06-12 22:54:29,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:54:29,662] [INFO] Task started: CheckM
[2023-06-12 22:54:29,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425205.1_ASM2242520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425205.1_ASM2242520v1_genomic.fna/checkm_input GCA_022425205.1_ASM2242520v1_genomic.fna/checkm_result
[2023-06-12 22:55:11,932] [INFO] Task succeeded: CheckM
[2023-06-12 22:55:11,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.91%
Contamintation: 5.30%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:55:11,958] [INFO] ===== Completeness check finished =====
[2023-06-12 22:55:11,958] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:55:11,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425205.1_ASM2242520v1_genomic.fna/markers.fasta)
[2023-06-12 22:55:11,959] [INFO] Task started: Blastn
[2023-06-12 22:55:11,959] [INFO] Running command: blastn -query GCA_022425205.1_ASM2242520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12a8098-fceb-4cb3-a156-a5ae4dbf74ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425205.1_ASM2242520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:55:12,724] [INFO] Task succeeded: Blastn
[2023-06-12 22:55:12,729] [INFO] Selected 11 target genomes.
[2023-06-12 22:55:12,729] [INFO] Target genome list was writen to GCA_022425205.1_ASM2242520v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:55:12,737] [INFO] Task started: fastANI
[2023-06-12 22:55:12,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg368dace9-5f33-4442-9e50-84cfc1524037/GCA_022425205.1_ASM2242520v1_genomic.fna.gz --refList GCA_022425205.1_ASM2242520v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425205.1_ASM2242520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:55:24,665] [INFO] Task succeeded: fastANI
[2023-06-12 22:55:24,676] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 22:55:24,677] [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_002690925.1	s__Rubripirellula sp002690925	99.261	990	1117	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002689655.1	s__Rubripirellula sp002689655	85.3319	941	1117	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002712845.1	s__Rubripirellula sp002712845	84.9458	391	1117	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003513555.1	s__Rubripirellula sp003513555	82.7161	832	1117	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	80.6408	578	1117	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270065.1	s__Rubripirellula sp012270065	78.0498	256	1117	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	98.24	98.24	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-12 22:55:24,679] [INFO] GTDB search result was written to GCA_022425205.1_ASM2242520v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:55:24,679] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:55:24,682] [INFO] DFAST_QC result json was written to GCA_022425205.1_ASM2242520v1_genomic.fna/dqc_result.json
[2023-06-12 22:55:24,682] [INFO] DFAST_QC completed!
[2023-06-12 22:55:24,682] [INFO] Total running time: 0h1m25s