[2023-06-30 05:31:09,822] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:31:09,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:31:09,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference
[2023-06-30 05:31:11,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:31:11,039] [INFO] Task started: Prodigal
[2023-06-30 05:31:11,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8501f1f-aafd-46b8-a93c-f63b46d65246/GCA_016714445.1_ASM1671444v1_genomic.fna.gz | prodigal -d GCA_016714445.1_ASM1671444v1_genomic.fna/cds.fna -a GCA_016714445.1_ASM1671444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:31:37,268] [INFO] Task succeeded: Prodigal
[2023-06-30 05:31:37,269] [INFO] Task started: HMMsearch
[2023-06-30 05:31:37,269] [INFO] Running command: hmmsearch --tblout GCA_016714445.1_ASM1671444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference/reference_markers.hmm GCA_016714445.1_ASM1671444v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:31:37,606] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:31:37,607] [INFO] Found 6/6 markers.
[2023-06-30 05:31:37,663] [INFO] Query marker FASTA was written to GCA_016714445.1_ASM1671444v1_genomic.fna/markers.fasta
[2023-06-30 05:31:37,664] [INFO] Task started: Blastn
[2023-06-30 05:31:37,664] [INFO] Running command: blastn -query GCA_016714445.1_ASM1671444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference/reference_markers.fasta -out GCA_016714445.1_ASM1671444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:31:38,350] [INFO] Task succeeded: Blastn
[2023-06-30 05:31:38,353] [INFO] Selected 28 target genomes.
[2023-06-30 05:31:38,354] [INFO] Target genome list was writen to GCA_016714445.1_ASM1671444v1_genomic.fna/target_genomes.txt
[2023-06-30 05:31:38,359] [INFO] Task started: fastANI
[2023-06-30 05:31:38,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8501f1f-aafd-46b8-a93c-f63b46d65246/GCA_016714445.1_ASM1671444v1_genomic.fna.gz --refList GCA_016714445.1_ASM1671444v1_genomic.fna/target_genomes.txt --output GCA_016714445.1_ASM1671444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:31:56,237] [INFO] Task succeeded: fastANI
[2023-06-30 05:31:56,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:31:56,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:31:56,240] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:31:56,240] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:31:56,241] [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
--------------------------------------------------------------------------------
[2023-06-30 05:31:56,243] [INFO] DFAST Taxonomy check result was written to GCA_016714445.1_ASM1671444v1_genomic.fna/tc_result.tsv
[2023-06-30 05:31:56,243] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:31:56,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:31:56,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference/checkm_data
[2023-06-30 05:31:56,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:31:56,311] [INFO] Task started: CheckM
[2023-06-30 05:31:56,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016714445.1_ASM1671444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016714445.1_ASM1671444v1_genomic.fna/checkm_input GCA_016714445.1_ASM1671444v1_genomic.fna/checkm_result
[2023-06-30 05:33:13,200] [INFO] Task succeeded: CheckM
[2023-06-30 05:33:13,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:33:13,221] [INFO] ===== Completeness check finished =====
[2023-06-30 05:33:13,221] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:33:13,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016714445.1_ASM1671444v1_genomic.fna/markers.fasta)
[2023-06-30 05:33:13,222] [INFO] Task started: Blastn
[2023-06-30 05:33:13,222] [INFO] Running command: blastn -query GCA_016714445.1_ASM1671444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ab746c4-ff24-47f0-8743-df794f9462b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_016714445.1_ASM1671444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:33:13,950] [INFO] Task succeeded: Blastn
[2023-06-30 05:33:13,956] [INFO] Selected 20 target genomes.
[2023-06-30 05:33:13,956] [INFO] Target genome list was writen to GCA_016714445.1_ASM1671444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:33:13,967] [INFO] Task started: fastANI
[2023-06-30 05:33:13,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8501f1f-aafd-46b8-a93c-f63b46d65246/GCA_016714445.1_ASM1671444v1_genomic.fna.gz --refList GCA_016714445.1_ASM1671444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016714445.1_ASM1671444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:33:28,987] [INFO] Task succeeded: fastANI
[2023-06-30 05:33:29,004] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:33:29,004] [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_016714445.1	s__OLB9 sp016714445	100.0	2080	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	97.58	97.50	0.85	0.84	3	conclusive
GCA_002482845.1	s__OLB9 sp002482845	79.8517	342	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714785.1	s__OLB9 sp016714785	78.9055	336	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715985.1	s__OLB9 sp016715985	78.7293	250	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717145.1	s__OLB9 sp016717145	78.5306	286	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714895.1	s__OLB9 sp016714895	77.7365	122	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715245.1	s__OLB9 sp016715245	77.4017	117	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	99.11	98.72	0.92	0.89	11	-
GCA_016722285.1	s__OLB9 sp016722285	77.2078	225	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	99.21	99.21	0.93	0.93	2	-
GCA_016717105.1	s__OLB9 sp016717105	77.0386	190	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	97.71	97.46	0.85	0.81	9	-
GCA_014379665.1	s__OLB9 sp014379665	76.8118	149	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716335.1	s__OLB9 sp016716335	76.7194	70	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136675.1	s__OLB9 sp019136675	76.4067	86	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567255.1	s__OLB9 sp001567255	76.2268	73	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708265.1	s__JADJGA01 sp016708265	76.0714	52	2081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJGA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:33:29,006] [INFO] GTDB search result was written to GCA_016714445.1_ASM1671444v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:33:29,007] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:33:29,010] [INFO] DFAST_QC result json was written to GCA_016714445.1_ASM1671444v1_genomic.fna/dqc_result.json
[2023-06-30 05:33:29,010] [INFO] DFAST_QC completed!
[2023-06-30 05:33:29,010] [INFO] Total running time: 0h2m19s