[2023-07-01 02:28:18,669] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:28:18,671] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:28:18,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference
[2023-07-01 02:28:19,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:28:19,895] [INFO] Task started: Prodigal
[2023-07-01 02:28:19,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg045f0c24-8480-442c-9c16-3927f9c81afd/GCA_016932775.1_ASM1693277v1_genomic.fna.gz | prodigal -d GCA_016932775.1_ASM1693277v1_genomic.fna/cds.fna -a GCA_016932775.1_ASM1693277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:28:29,759] [INFO] Task succeeded: Prodigal
[2023-07-01 02:28:29,760] [INFO] Task started: HMMsearch
[2023-07-01 02:28:29,760] [INFO] Running command: hmmsearch --tblout GCA_016932775.1_ASM1693277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference/reference_markers.hmm GCA_016932775.1_ASM1693277v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:28:29,980] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:28:29,981] [INFO] Found 6/6 markers.
[2023-07-01 02:28:30,014] [INFO] Query marker FASTA was written to GCA_016932775.1_ASM1693277v1_genomic.fna/markers.fasta
[2023-07-01 02:28:30,015] [INFO] Task started: Blastn
[2023-07-01 02:28:30,015] [INFO] Running command: blastn -query GCA_016932775.1_ASM1693277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference/reference_markers.fasta -out GCA_016932775.1_ASM1693277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:28:30,595] [INFO] Task succeeded: Blastn
[2023-07-01 02:28:30,599] [INFO] Selected 27 target genomes.
[2023-07-01 02:28:30,599] [INFO] Target genome list was writen to GCA_016932775.1_ASM1693277v1_genomic.fna/target_genomes.txt
[2023-07-01 02:28:30,601] [INFO] Task started: fastANI
[2023-07-01 02:28:30,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg045f0c24-8480-442c-9c16-3927f9c81afd/GCA_016932775.1_ASM1693277v1_genomic.fna.gz --refList GCA_016932775.1_ASM1693277v1_genomic.fna/target_genomes.txt --output GCA_016932775.1_ASM1693277v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:28:47,068] [INFO] Task succeeded: fastANI
[2023-07-01 02:28:47,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:28:47,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:28:47,072] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:28:47,072] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:28:47,072] [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
Desulfatiglans anilini	strain=DSM 4660	GCA_000422285.1	90728	90728	type	True	75.934	65	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:28:47,074] [INFO] DFAST Taxonomy check result was written to GCA_016932775.1_ASM1693277v1_genomic.fna/tc_result.tsv
[2023-07-01 02:28:47,075] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:28:47,075] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:28:47,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference/checkm_data
[2023-07-01 02:28:47,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:28:47,117] [INFO] Task started: CheckM
[2023-07-01 02:28:47,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016932775.1_ASM1693277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016932775.1_ASM1693277v1_genomic.fna/checkm_input GCA_016932775.1_ASM1693277v1_genomic.fna/checkm_result
[2023-07-01 02:29:19,480] [INFO] Task succeeded: CheckM
[2023-07-01 02:29:19,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:29:19,500] [INFO] ===== Completeness check finished =====
[2023-07-01 02:29:19,500] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:29:19,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016932775.1_ASM1693277v1_genomic.fna/markers.fasta)
[2023-07-01 02:29:19,500] [INFO] Task started: Blastn
[2023-07-01 02:29:19,500] [INFO] Running command: blastn -query GCA_016932775.1_ASM1693277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccfd13df-982e-4d60-8c34-8f0784990387/dqc_reference/reference_markers_gtdb.fasta -out GCA_016932775.1_ASM1693277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:29:20,335] [INFO] Task succeeded: Blastn
[2023-07-01 02:29:20,340] [INFO] Selected 34 target genomes.
[2023-07-01 02:29:20,340] [INFO] Target genome list was writen to GCA_016932775.1_ASM1693277v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:29:20,398] [INFO] Task started: fastANI
[2023-07-01 02:29:20,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg045f0c24-8480-442c-9c16-3927f9c81afd/GCA_016932775.1_ASM1693277v1_genomic.fna.gz --refList GCA_016932775.1_ASM1693277v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016932775.1_ASM1693277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:29:40,687] [INFO] Task succeeded: fastANI
[2023-07-01 02:29:40,692] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 02:29:40,693] [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_016926135.1	s__HGW-15 sp016926135	76.9578	150	1133	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__HGW-15;g__HGW-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840535.1	s__HGW-15 sp002840535	76.3731	88	1133	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__HGW-15;g__HGW-15	95.0	95.55	95.55	0.86	0.86	2	-
GCA_011367735.1	s__DSXZ01 sp011367735	76.2448	78	1133	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__HGW-15;g__DSXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422285.1	s__Desulfatiglans anilini	75.934	65	1133	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfatiglans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:29:40,695] [INFO] GTDB search result was written to GCA_016932775.1_ASM1693277v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:29:40,695] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:29:40,697] [INFO] DFAST_QC result json was written to GCA_016932775.1_ASM1693277v1_genomic.fna/dqc_result.json
[2023-07-01 02:29:40,697] [INFO] DFAST_QC completed!
[2023-07-01 02:29:40,698] [INFO] Total running time: 0h1m22s