[2024-01-24 13:58:42,300] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference
[2024-01-24 13:58:43,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,731] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,731] [INFO] Running command: gunzip -c /var/lib/cwl/stgadaedb98-4daf-4477-bd3a-fcd4ba2fbd49/GCF_000313175.2_ASM31317v2_genomic.fna.gz | prodigal -d GCF_000313175.2_ASM31317v2_genomic.fna/cds.fna -a GCF_000313175.2_ASM31317v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:53,340] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:53,341] [INFO] Task started: HMMsearch
[2024-01-24 13:58:53,341] [INFO] Running command: hmmsearch --tblout GCF_000313175.2_ASM31317v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference/reference_markers.hmm GCF_000313175.2_ASM31317v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:53,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:53,626] [INFO] Found 6/6 markers.
[2024-01-24 13:58:53,665] [INFO] Query marker FASTA was written to GCF_000313175.2_ASM31317v2_genomic.fna/markers.fasta
[2024-01-24 13:58:53,666] [INFO] Task started: Blastn
[2024-01-24 13:58:53,666] [INFO] Running command: blastn -query GCF_000313175.2_ASM31317v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference/reference_markers.fasta -out GCF_000313175.2_ASM31317v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:54,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:54,293] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:54,293] [INFO] Target genome list was writen to GCF_000313175.2_ASM31317v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:54,297] [INFO] Task started: fastANI
[2024-01-24 13:58:54,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgadaedb98-4daf-4477-bd3a-fcd4ba2fbd49/GCF_000313175.2_ASM31317v2_genomic.fna.gz --refList GCF_000313175.2_ASM31317v2_genomic.fna/target_genomes.txt --output GCF_000313175.2_ASM31317v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:03,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:03,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:03,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:03,216] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:03,216] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:03,216] [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 santarosai	strain=LT 821	GCA_000313175.2	28183	28183	type	True	100.0	1326	1326	95	conclusive
Leptospira alexanderi	strain=L 60	GCA_000243815.3	100053	100053	type	True	87.4859	1039	1326	95	below_threshold
Leptospira mayottensis	strain=200901116	GCA_000306675.3	1137606	1137606	type	True	86.6838	1060	1326	95	below_threshold
Leptospira borgpetersenii	strain=DSM 21538	GCA_003046425.1	174	174	type	True	86.6066	1031	1326	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	82.9304	977	1326	95	below_threshold
Leptospira kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	81.2685	838	1326	95	below_threshold
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	80.5204	805	1326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,218] [INFO] DFAST Taxonomy check result was written to GCF_000313175.2_ASM31317v2_genomic.fna/tc_result.tsv
[2024-01-24 13:59:03,219] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:03,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:03,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference/checkm_data
[2024-01-24 13:59:03,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:03,258] [INFO] Task started: CheckM
[2024-01-24 13:59:03,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000313175.2_ASM31317v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000313175.2_ASM31317v2_genomic.fna/checkm_input GCF_000313175.2_ASM31317v2_genomic.fna/checkm_result
[2024-01-24 13:59:34,788] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:34,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:34,804] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:34,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:34,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000313175.2_ASM31317v2_genomic.fna/markers.fasta)
[2024-01-24 13:59:34,805] [INFO] Task started: Blastn
[2024-01-24 13:59:34,805] [INFO] Running command: blastn -query GCF_000313175.2_ASM31317v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg221cefc9-5455-4876-b711-a9ef3c5edf0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000313175.2_ASM31317v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:35,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:35,613] [INFO] Selected 7 target genomes.
[2024-01-24 13:59:35,613] [INFO] Target genome list was writen to GCF_000313175.2_ASM31317v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:35,623] [INFO] Task started: fastANI
[2024-01-24 13:59:35,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgadaedb98-4daf-4477-bd3a-fcd4ba2fbd49/GCF_000313175.2_ASM31317v2_genomic.fna.gz --refList GCF_000313175.2_ASM31317v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000313175.2_ASM31317v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:44,697] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:44,708] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:44,709] [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_000313175.2	s__Leptospira santarosai	100.0	1326	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.62	96.47	0.92	0.90	43	conclusive
GCF_000243815.2	s__Leptospira alexanderi	87.5129	1038	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.22	97.61	0.97	0.93	6	-
GCF_000244815.1	s__Leptospira weilii	86.8764	1047	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	95.50	95.12	0.87	0.84	20	-
GCF_000306675.2	s__Leptospira mayottensis	86.6429	1064	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.59	98.88	0.95	0.90	6	-
GCF_003046425.1	s__Leptospira borgpetersenii	86.5852	1033	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.13	97.82	0.96	0.92	148	-
GCF_000332415.1	s__Leptospira weilii_A	83.1104	938	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347175.1	s__Leptospira alstonii	82.9456	974	1326	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:44,713] [INFO] GTDB search result was written to GCF_000313175.2_ASM31317v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:44,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:44,717] [INFO] DFAST_QC result json was written to GCF_000313175.2_ASM31317v2_genomic.fna/dqc_result.json
[2024-01-24 13:59:44,717] [INFO] DFAST_QC completed!
[2024-01-24 13:59:44,717] [INFO] Total running time: 0h1m2s