[2024-01-25 19:40:35,456] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:35,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:35,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference
[2024-01-25 19:40:36,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:36,644] [INFO] Task started: Prodigal
[2024-01-25 19:40:36,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg1216b37c-aa6d-450c-be0d-efae1be0fe2d/GCF_002812085.1_ASM281208v1_genomic.fna.gz | prodigal -d GCF_002812085.1_ASM281208v1_genomic.fna/cds.fna -a GCF_002812085.1_ASM281208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:45,087] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:45,088] [INFO] Task started: HMMsearch
[2024-01-25 19:40:45,088] [INFO] Running command: hmmsearch --tblout GCF_002812085.1_ASM281208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference/reference_markers.hmm GCF_002812085.1_ASM281208v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:45,322] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:45,325] [INFO] Found 6/6 markers.
[2024-01-25 19:40:45,356] [INFO] Query marker FASTA was written to GCF_002812085.1_ASM281208v1_genomic.fna/markers.fasta
[2024-01-25 19:40:45,356] [INFO] Task started: Blastn
[2024-01-25 19:40:45,357] [INFO] Running command: blastn -query GCF_002812085.1_ASM281208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference/reference_markers.fasta -out GCF_002812085.1_ASM281208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:45,884] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:45,886] [INFO] Selected 10 target genomes.
[2024-01-25 19:40:45,887] [INFO] Target genome list was writen to GCF_002812085.1_ASM281208v1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:45,890] [INFO] Task started: fastANI
[2024-01-25 19:40:45,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg1216b37c-aa6d-450c-be0d-efae1be0fe2d/GCF_002812085.1_ASM281208v1_genomic.fna.gz --refList GCF_002812085.1_ASM281208v1_genomic.fna/target_genomes.txt --output GCF_002812085.1_ASM281208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:53,889] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:53,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:53,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:53,896] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:40:53,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:53,896] [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
Leptospira levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	100.0	1284	1285	95	conclusive
Leptospira ellinghausenii	strain=E18	GCA_003114815.1	1917822	1917822	type	True	91.95	1186	1285	95	below_threshold
Leptospira biflexa	strain=Patoc 1 (Paris)	GCA_000017685.1	172	172	type	True	83.4531	967	1285	95	below_threshold
Leptospira yanagawae	strain=Sao Paulo	GCA_000332475.2	293069	293069	type	True	83.2224	951	1285	95	below_threshold
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	81.1792	765	1285	95	below_threshold
Leptospira vanthielii	strain=Waz Holland	GCA_000332455.2	293085	293085	type	True	80.9708	741	1285	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	80.9467	737	1285	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	80.8963	753	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:53,898] [INFO] DFAST Taxonomy check result was written to GCF_002812085.1_ASM281208v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:53,898] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:53,898] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:53,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference/checkm_data
[2024-01-25 19:40:53,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:53,942] [INFO] Task started: CheckM
[2024-01-25 19:40:53,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002812085.1_ASM281208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002812085.1_ASM281208v1_genomic.fna/checkm_input GCF_002812085.1_ASM281208v1_genomic.fna/checkm_result
[2024-01-25 19:41:23,804] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:23,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:23,868] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:23,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:23,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002812085.1_ASM281208v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:23,869] [INFO] Task started: Blastn
[2024-01-25 19:41:23,869] [INFO] Running command: blastn -query GCF_002812085.1_ASM281208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd6059c-7bea-47df-a321-db7abe52c17c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002812085.1_ASM281208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:24,682] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:24,685] [INFO] Selected 8 target genomes.
[2024-01-25 19:41:24,685] [INFO] Target genome list was writen to GCF_002812085.1_ASM281208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:24,697] [INFO] Task started: fastANI
[2024-01-25 19:41:24,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg1216b37c-aa6d-450c-be0d-efae1be0fe2d/GCF_002812085.1_ASM281208v1_genomic.fna.gz --refList GCF_002812085.1_ASM281208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002812085.1_ASM281208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:32,171] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:32,177] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:32,177] [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
GCF_002812085.1	s__Leptospira_A levettii	100.0	1284	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.63	98.25	0.94	0.91	14	conclusive
GCF_003114815.1	s__Leptospira_A ellinghausenii	91.95	1186	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742255.1	s__Leptospira_A sp016742255	91.9183	1130	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769665.1	s__Leptospira_A kemamanensis	84.5527	974	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769525.1	s__Leptospira_A bouyouniensis	83.4922	997	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.10	99.07	0.94	0.93	3	-
GCF_000017685.1	s__Leptospira_A biflexa	83.4483	967	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.66	98.34	0.97	0.95	7	-
GCF_004769635.1	s__Leptospira_A jelokensis	83.3417	938	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.57	98.57	0.95	0.95	2	-
GCF_000332475.2	s__Leptospira_A yanagawae	83.2408	949	1285	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.50	98.50	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:32,179] [INFO] GTDB search result was written to GCF_002812085.1_ASM281208v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:32,179] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:32,181] [INFO] DFAST_QC result json was written to GCF_002812085.1_ASM281208v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:32,182] [INFO] DFAST_QC completed!
[2024-01-25 19:41:32,182] [INFO] Total running time: 0h0m57s