[2023-06-13 05:12:18,926] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:12:18,929] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:12:18,929] [INFO] DQC Reference Directory: /var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference
[2023-06-13 05:12:20,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:12:20,231] [INFO] Task started: Prodigal
[2023-06-13 05:12:20,232] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ef6e7aa-6e36-4a4d-a81f-8c8fefa5904b/GCA_022014255.1_ASM2201425v1_genomic.fna.gz | prodigal -d GCA_022014255.1_ASM2201425v1_genomic.fna/cds.fna -a GCA_022014255.1_ASM2201425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:12:24,338] [INFO] Task succeeded: Prodigal
[2023-06-13 05:12:24,339] [INFO] Task started: HMMsearch
[2023-06-13 05:12:24,339] [INFO] Running command: hmmsearch --tblout GCA_022014255.1_ASM2201425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference/reference_markers.hmm GCA_022014255.1_ASM2201425v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:12:24,570] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:12:24,571] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3ef6e7aa-6e36-4a4d-a81f-8c8fefa5904b/GCA_022014255.1_ASM2201425v1_genomic.fna.gz]
[2023-06-13 05:12:24,598] [INFO] Query marker FASTA was written to GCA_022014255.1_ASM2201425v1_genomic.fna/markers.fasta
[2023-06-13 05:12:24,598] [INFO] Task started: Blastn
[2023-06-13 05:12:24,598] [INFO] Running command: blastn -query GCA_022014255.1_ASM2201425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference/reference_markers.fasta -out GCA_022014255.1_ASM2201425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:12:25,085] [INFO] Task succeeded: Blastn
[2023-06-13 05:12:25,089] [INFO] Selected 19 target genomes.
[2023-06-13 05:12:25,090] [INFO] Target genome list was writen to GCA_022014255.1_ASM2201425v1_genomic.fna/target_genomes.txt
[2023-06-13 05:12:25,094] [INFO] Task started: fastANI
[2023-06-13 05:12:25,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ef6e7aa-6e36-4a4d-a81f-8c8fefa5904b/GCA_022014255.1_ASM2201425v1_genomic.fna.gz --refList GCA_022014255.1_ASM2201425v1_genomic.fna/target_genomes.txt --output GCA_022014255.1_ASM2201425v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:12:35,153] [INFO] Task succeeded: fastANI
[2023-06-13 05:12:35,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:12:35,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:12:35,157] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:12:35,157] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:12:35,158] [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
--------------------------------------------------------------------------------
[2023-06-13 05:12:35,160] [INFO] DFAST Taxonomy check result was written to GCA_022014255.1_ASM2201425v1_genomic.fna/tc_result.tsv
[2023-06-13 05:12:35,161] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:12:35,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:12:35,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference/checkm_data
[2023-06-13 05:12:35,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:12:35,190] [INFO] Task started: CheckM
[2023-06-13 05:12:35,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022014255.1_ASM2201425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022014255.1_ASM2201425v1_genomic.fna/checkm_input GCA_022014255.1_ASM2201425v1_genomic.fna/checkm_result
[2023-06-13 05:12:55,323] [INFO] Task succeeded: CheckM
[2023-06-13 05:12:55,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:12:55,341] [INFO] ===== Completeness check finished =====
[2023-06-13 05:12:55,342] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:12:55,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022014255.1_ASM2201425v1_genomic.fna/markers.fasta)
[2023-06-13 05:12:55,342] [INFO] Task started: Blastn
[2023-06-13 05:12:55,343] [INFO] Running command: blastn -query GCA_022014255.1_ASM2201425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34f05cc-71ec-48c3-8d15-f3b846aa9fc6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022014255.1_ASM2201425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:12:55,799] [INFO] Task succeeded: Blastn
[2023-06-13 05:12:55,803] [INFO] Selected 10 target genomes.
[2023-06-13 05:12:55,803] [INFO] Target genome list was writen to GCA_022014255.1_ASM2201425v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:12:55,809] [INFO] Task started: fastANI
[2023-06-13 05:12:55,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ef6e7aa-6e36-4a4d-a81f-8c8fefa5904b/GCA_022014255.1_ASM2201425v1_genomic.fna.gz --refList GCA_022014255.1_ASM2201425v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022014255.1_ASM2201425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:13:02,575] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:02,589] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:13:02,589] [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_013792055.1	s__B13-G4 sp013792055	97.5078	437	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4	95.0	99.03	97.50	0.88	0.84	10	conclusive
GCA_018897415.1	s__B13-G4 sp018897415	88.9523	311	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4	95.0	99.07	99.07	0.81	0.81	2	-
GCA_014237365.1	s__B13-G4 sp014237365	85.8175	312	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003647525.1	s__B13-G4 sp003647525	85.5662	175	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013202725.1	s__Desulfaltia sp013202725	79.0137	82	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__Desulfaltia	95.0	96.32	96.29	0.80	0.79	3	-
GCA_004193555.1	s__ETH-SRB1 sp004193555	78.2786	122	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__ETH-SRB1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381545.1	s__Desulfaltia bathyphila	77.2807	119	546	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__Desulfaltia	95.0	99.82	99.78	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-13 05:13:02,591] [INFO] GTDB search result was written to GCA_022014255.1_ASM2201425v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:13:02,592] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:13:02,594] [INFO] DFAST_QC result json was written to GCA_022014255.1_ASM2201425v1_genomic.fna/dqc_result.json
[2023-06-13 05:13:02,595] [INFO] DFAST_QC completed!
[2023-06-13 05:13:02,595] [INFO] Total running time: 0h0m44s