[2023-06-13 11:29:46,512] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:29:46,514] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:29:46,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference
[2023-06-13 11:29:47,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:29:47,851] [INFO] Task started: Prodigal
[2023-06-13 11:29:47,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg6962668b-3443-4373-88c6-6981fc4e8b44/GCA_022708025.1_ASM2270802v1_genomic.fna.gz | prodigal -d GCA_022708025.1_ASM2270802v1_genomic.fna/cds.fna -a GCA_022708025.1_ASM2270802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:29:53,522] [INFO] Task succeeded: Prodigal
[2023-06-13 11:29:53,522] [INFO] Task started: HMMsearch
[2023-06-13 11:29:53,522] [INFO] Running command: hmmsearch --tblout GCA_022708025.1_ASM2270802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference/reference_markers.hmm GCA_022708025.1_ASM2270802v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:29:53,808] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:29:53,810] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6962668b-3443-4373-88c6-6981fc4e8b44/GCA_022708025.1_ASM2270802v1_genomic.fna.gz]
[2023-06-13 11:29:53,844] [INFO] Query marker FASTA was written to GCA_022708025.1_ASM2270802v1_genomic.fna/markers.fasta
[2023-06-13 11:29:53,844] [INFO] Task started: Blastn
[2023-06-13 11:29:53,845] [INFO] Running command: blastn -query GCA_022708025.1_ASM2270802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference/reference_markers.fasta -out GCA_022708025.1_ASM2270802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:29:54,477] [INFO] Task succeeded: Blastn
[2023-06-13 11:29:54,481] [INFO] Selected 16 target genomes.
[2023-06-13 11:29:54,481] [INFO] Target genome list was writen to GCA_022708025.1_ASM2270802v1_genomic.fna/target_genomes.txt
[2023-06-13 11:29:54,487] [INFO] Task started: fastANI
[2023-06-13 11:29:54,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg6962668b-3443-4373-88c6-6981fc4e8b44/GCA_022708025.1_ASM2270802v1_genomic.fna.gz --refList GCA_022708025.1_ASM2270802v1_genomic.fna/target_genomes.txt --output GCA_022708025.1_ASM2270802v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:04,662] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:04,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:04,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:04,668] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:30:04,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:30:04,668] [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
Ignavibacterium album	strain=JCM 16511	GCA_000258405.1	591197	591197	type	True	76.5802	233	1099	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:30:04,671] [INFO] DFAST Taxonomy check result was written to GCA_022708025.1_ASM2270802v1_genomic.fna/tc_result.tsv
[2023-06-13 11:30:04,672] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:04,672] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:04,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference/checkm_data
[2023-06-13 11:30:04,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:04,716] [INFO] Task started: CheckM
[2023-06-13 11:30:04,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708025.1_ASM2270802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708025.1_ASM2270802v1_genomic.fna/checkm_input GCA_022708025.1_ASM2270802v1_genomic.fna/checkm_result
[2023-06-13 11:30:29,704] [INFO] Task succeeded: CheckM
[2023-06-13 11:30:29,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:30:29,737] [INFO] ===== Completeness check finished =====
[2023-06-13 11:30:29,737] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:30:29,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708025.1_ASM2270802v1_genomic.fna/markers.fasta)
[2023-06-13 11:30:29,738] [INFO] Task started: Blastn
[2023-06-13 11:30:29,738] [INFO] Running command: blastn -query GCA_022708025.1_ASM2270802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2edaf89d-e2fd-4c2e-b893-9b9dabd1971b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708025.1_ASM2270802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:30,579] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:30,584] [INFO] Selected 10 target genomes.
[2023-06-13 11:30:30,584] [INFO] Target genome list was writen to GCA_022708025.1_ASM2270802v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:30:30,610] [INFO] Task started: fastANI
[2023-06-13 11:30:30,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg6962668b-3443-4373-88c6-6981fc4e8b44/GCA_022708025.1_ASM2270802v1_genomic.fna.gz --refList GCA_022708025.1_ASM2270802v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708025.1_ASM2270802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:30:38,015] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:38,032] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:30:38,033] [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_002050295.1	s__IGN3 sp002050295	99.9001	1048	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	99.89	99.89	0.88	0.88	2	conclusive
GCA_013285425.1	s__IGN3 sp900696555	82.7532	837	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	99.37	98.46	0.95	0.86	4	-
GCA_016707585.1	s__IGN3 sp016707585	78.1756	410	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707115.1	s__IGN3 sp016707115	78.0646	384	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	98.99	98.99	0.85	0.85	2	-
GCA_003538625.1	s__IGN3 sp003538625	77.8345	347	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018059515.1	s__IGN3 sp018059515	77.7564	334	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709765.1	s__IGN3 sp016709765	77.5288	369	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011329055.1	s__Ignavibacterium album_B	76.6113	210	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700155.1	s__GCA-016700155 sp016700155	76.1889	144	1099	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__GCA-016700155	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:30:38,036] [INFO] GTDB search result was written to GCA_022708025.1_ASM2270802v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:30:38,037] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:30:38,041] [INFO] DFAST_QC result json was written to GCA_022708025.1_ASM2270802v1_genomic.fna/dqc_result.json
[2023-06-13 11:30:38,042] [INFO] DFAST_QC completed!
[2023-06-13 11:30:38,042] [INFO] Total running time: 0h0m52s