[2024-01-25 17:35:20,509] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:20,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:20,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference
[2024-01-25 17:35:21,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:21,658] [INFO] Task started: Prodigal
[2024-01-25 17:35:21,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg7df78bc4-f7f8-49f8-bb6f-641f41e89813/GCF_000243735.2_gls454052v1.0_genomic.fna.gz | prodigal -d GCF_000243735.2_gls454052v1.0_genomic.fna/cds.fna -a GCF_000243735.2_gls454052v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:30,939] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:30,939] [INFO] Task started: HMMsearch
[2024-01-25 17:35:30,939] [INFO] Running command: hmmsearch --tblout GCF_000243735.2_gls454052v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference/reference_markers.hmm GCF_000243735.2_gls454052v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:31,196] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:31,198] [INFO] Found 6/6 markers.
[2024-01-25 17:35:31,235] [INFO] Query marker FASTA was written to GCF_000243735.2_gls454052v1.0_genomic.fna/markers.fasta
[2024-01-25 17:35:31,236] [INFO] Task started: Blastn
[2024-01-25 17:35:31,236] [INFO] Running command: blastn -query GCF_000243735.2_gls454052v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference/reference_markers.fasta -out GCF_000243735.2_gls454052v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:31,821] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:31,824] [INFO] Selected 9 target genomes.
[2024-01-25 17:35:31,824] [INFO] Target genome list was writen to GCF_000243735.2_gls454052v1.0_genomic.fna/target_genomes.txt
[2024-01-25 17:35:31,827] [INFO] Task started: fastANI
[2024-01-25 17:35:31,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg7df78bc4-f7f8-49f8-bb6f-641f41e89813/GCF_000243735.2_gls454052v1.0_genomic.fna.gz --refList GCF_000243735.2_gls454052v1.0_genomic.fna/target_genomes.txt --output GCF_000243735.2_gls454052v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:41,422] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:41,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:41,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:41,429] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:41,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:41,429] [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 kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	100.0	1471	1471	95	conclusive
Leptospira barantonii	strain=FH4-C-A1	GCA_002811925.1	2023184	2023184	type	True	90.9065	1346	1471	95	below_threshold
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	84.4901	1183	1471	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	82.9776	952	1471	95	below_threshold
Leptospira adleri	strain=FH2-B-D1	GCA_002811985.1	2023186	2023186	type	True	81.7485	967	1471	95	below_threshold
Leptospira santarosai	strain=LT 821	GCA_000313175.2	28183	28183	type	True	81.4036	833	1471	95	below_threshold
Leptospira tipperaryensis	strain=GWTS #1	GCA_001729245.1	2564040	2564040	type	True	81.324	1052	1471	95	below_threshold
Leptospira ellisii	strain=ATI7-C-A5	GCA_002811955.1	2023197	2023197	type	True	80.6539	750	1471	95	below_threshold
Leptospira kirschneri	strain=3522 CT	GCA_000243695.3	29507	29507	type	True	79.8096	745	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:41,431] [INFO] DFAST Taxonomy check result was written to GCF_000243735.2_gls454052v1.0_genomic.fna/tc_result.tsv
[2024-01-25 17:35:41,432] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:41,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:41,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference/checkm_data
[2024-01-25 17:35:41,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:41,474] [INFO] Task started: CheckM
[2024-01-25 17:35:41,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243735.2_gls454052v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243735.2_gls454052v1.0_genomic.fna/checkm_input GCF_000243735.2_gls454052v1.0_genomic.fna/checkm_result
[2024-01-25 17:36:11,540] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:11,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:11,560] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:11,561] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:11,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243735.2_gls454052v1.0_genomic.fna/markers.fasta)
[2024-01-25 17:36:11,562] [INFO] Task started: Blastn
[2024-01-25 17:36:11,562] [INFO] Running command: blastn -query GCF_000243735.2_gls454052v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg80636f00-49b7-4fef-ae94-0c041b866814/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243735.2_gls454052v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:12,382] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:12,384] [INFO] Selected 9 target genomes.
[2024-01-25 17:36:12,385] [INFO] Target genome list was writen to GCF_000243735.2_gls454052v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:12,389] [INFO] Task started: fastANI
[2024-01-25 17:36:12,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg7df78bc4-f7f8-49f8-bb6f-641f41e89813/GCF_000243735.2_gls454052v1.0_genomic.fna.gz --refList GCF_000243735.2_gls454052v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000243735.2_gls454052v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:21,490] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:21,497] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:21,497] [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_000243735.2	s__Leptospira kmetyi	100.0	1471	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.04	98.99	0.96	0.94	7	conclusive
GCF_002811925.1	s__Leptospira barantonii	90.9065	1346	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	96.36	96.36	0.93	0.93	2	-
GCF_003545925.1	s__Leptospira yasudae	84.473	1185	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	97.33	95.78	0.94	0.93	8	-
GCF_000347175.1	s__Leptospira alstonii	82.9508	955	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	-
GCF_000332415.1	s__Leptospira weilii_A	82.7408	971	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811985.1	s__Leptospira adleri	81.7628	965	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.11	98.26	0.94	0.91	3	-
GCF_000313175.2	s__Leptospira santarosai	81.3952	834	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.62	96.47	0.92	0.90	43	-
GCF_002811955.1	s__Leptospira ellisii	80.6653	749	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770155.1	s__Leptospira gomenensis	80.5415	850	1471	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.98	99.98	0.99	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:21,500] [INFO] GTDB search result was written to GCF_000243735.2_gls454052v1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:21,500] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:21,504] [INFO] DFAST_QC result json was written to GCF_000243735.2_gls454052v1.0_genomic.fna/dqc_result.json
[2024-01-25 17:36:21,504] [INFO] DFAST_QC completed!
[2024-01-25 17:36:21,504] [INFO] Total running time: 0h1m1s