[2023-06-05 10:33:39,082] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:39,085] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:39,085] [INFO] DQC Reference Directory: /var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference
[2023-06-05 10:33:42,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:42,401] [INFO] Task started: Prodigal
[2023-06-05 10:33:42,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg57885c8c-b61d-4011-ab86-d329d567e0c4/GCA_004556145.1_ASM455614v1_genomic.fna.gz | prodigal -d GCA_004556145.1_ASM455614v1_genomic.fna/cds.fna -a GCA_004556145.1_ASM455614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:33:46,277] [INFO] Task succeeded: Prodigal
[2023-06-05 10:33:46,277] [INFO] Task started: HMMsearch
[2023-06-05 10:33:46,277] [INFO] Running command: hmmsearch --tblout GCA_004556145.1_ASM455614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference/reference_markers.hmm GCA_004556145.1_ASM455614v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:33:46,475] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:33:46,476] [INFO] Found 6/6 markers.
[2023-06-05 10:33:46,497] [INFO] Query marker FASTA was written to GCA_004556145.1_ASM455614v1_genomic.fna/markers.fasta
[2023-06-05 10:33:46,498] [INFO] Task started: Blastn
[2023-06-05 10:33:46,498] [INFO] Running command: blastn -query GCA_004556145.1_ASM455614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference/reference_markers.fasta -out GCA_004556145.1_ASM455614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:33:47,544] [INFO] Task succeeded: Blastn
[2023-06-05 10:33:47,548] [INFO] Selected 20 target genomes.
[2023-06-05 10:33:47,549] [INFO] Target genome list was writen to GCA_004556145.1_ASM455614v1_genomic.fna/target_genomes.txt
[2023-06-05 10:33:47,555] [INFO] Task started: fastANI
[2023-06-05 10:33:47,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg57885c8c-b61d-4011-ab86-d329d567e0c4/GCA_004556145.1_ASM455614v1_genomic.fna.gz --refList GCA_004556145.1_ASM455614v1_genomic.fna/target_genomes.txt --output GCA_004556145.1_ASM455614v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:33:54,734] [INFO] Task succeeded: fastANI
[2023-06-05 10:33:54,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:33:54,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:33:54,737] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:33:54,737] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:33:54,737] [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
--------------------------------------------------------------------------------
[2023-06-05 10:33:54,739] [INFO] DFAST Taxonomy check result was written to GCA_004556145.1_ASM455614v1_genomic.fna/tc_result.tsv
[2023-06-05 10:33:54,740] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:33:54,740] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:33:54,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference/checkm_data
[2023-06-05 10:33:54,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:33:54,763] [INFO] Task started: CheckM
[2023-06-05 10:33:54,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004556145.1_ASM455614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004556145.1_ASM455614v1_genomic.fna/checkm_input GCA_004556145.1_ASM455614v1_genomic.fna/checkm_result
[2023-06-05 10:34:13,719] [INFO] Task succeeded: CheckM
[2023-06-05 10:34:13,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:34:13,739] [INFO] ===== Completeness check finished =====
[2023-06-05 10:34:13,740] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:34:13,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004556145.1_ASM455614v1_genomic.fna/markers.fasta)
[2023-06-05 10:34:13,740] [INFO] Task started: Blastn
[2023-06-05 10:34:13,740] [INFO] Running command: blastn -query GCA_004556145.1_ASM455614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2000e97-30cf-481b-a3f7-2067b4ba8268/dqc_reference/reference_markers_gtdb.fasta -out GCA_004556145.1_ASM455614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:14,501] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:14,505] [INFO] Selected 17 target genomes.
[2023-06-05 10:34:14,506] [INFO] Target genome list was writen to GCA_004556145.1_ASM455614v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:34:14,513] [INFO] Task started: fastANI
[2023-06-05 10:34:14,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg57885c8c-b61d-4011-ab86-d329d567e0c4/GCA_004556145.1_ASM455614v1_genomic.fna.gz --refList GCA_004556145.1_ASM455614v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004556145.1_ASM455614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:34:20,491] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:20,502] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:34:20,502] [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_001940855.1	s__Phil1 sp001940855	97.1842	405	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Phil1	95.0	97.09	96.81	0.92	0.85	14	conclusive
GCA_004558525.1	s__Phil1 sp004558525	80.1232	235	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Phil1	95.0	98.96	98.54	0.91	0.86	6	-
GCA_017435905.1	s__UBA1685 sp017435905	77.5326	50	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	98.49	98.49	0.94	0.94	2	-
GCA_015056105.1	s__UBA1685 sp015056105	77.4472	50	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320595.1	s__UBA1685 sp002320595	77.1062	70	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA1685	95.0	97.25	96.45	0.86	0.81	7	-
GCA_004557245.1	s__SFEL01 sp004557245	76.7023	53	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__SFEL01	95.0	97.48	96.14	0.90	0.84	17	-
--------------------------------------------------------------------------------
[2023-06-05 10:34:20,504] [INFO] GTDB search result was written to GCA_004556145.1_ASM455614v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:34:20,504] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:34:20,506] [INFO] DFAST_QC result json was written to GCA_004556145.1_ASM455614v1_genomic.fna/dqc_result.json
[2023-06-05 10:34:20,507] [INFO] DFAST_QC completed!
[2023-06-05 10:34:20,507] [INFO] Total running time: 0h0m41s