[2024-01-24 13:41:10,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference
[2024-01-24 13:41:12,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:12,237] [INFO] Task started: Prodigal
[2024-01-24 13:41:12,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg439fd421-c3bd-49ba-9f59-59a88b991984/GCF_000347175.1_gls454194v01_genomic.fna.gz | prodigal -d GCF_000347175.1_gls454194v01_genomic.fna/cds.fna -a GCF_000347175.1_gls454194v01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:22,219] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:22,220] [INFO] Task started: HMMsearch
[2024-01-24 13:41:22,220] [INFO] Running command: hmmsearch --tblout GCF_000347175.1_gls454194v01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference/reference_markers.hmm GCF_000347175.1_gls454194v01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:22,560] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:22,562] [INFO] Found 6/6 markers.
[2024-01-24 13:41:22,606] [INFO] Query marker FASTA was written to GCF_000347175.1_gls454194v01_genomic.fna/markers.fasta
[2024-01-24 13:41:22,607] [INFO] Task started: Blastn
[2024-01-24 13:41:22,607] [INFO] Running command: blastn -query GCF_000347175.1_gls454194v01_genomic.fna/markers.fasta -db /var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference/reference_markers.fasta -out GCF_000347175.1_gls454194v01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:23,254] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:23,257] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:23,258] [INFO] Target genome list was writen to GCF_000347175.1_gls454194v01_genomic.fna/target_genomes.txt
[2024-01-24 13:41:23,264] [INFO] Task started: fastANI
[2024-01-24 13:41:23,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg439fd421-c3bd-49ba-9f59-59a88b991984/GCF_000347175.1_gls454194v01_genomic.fna.gz --refList GCF_000347175.1_gls454194v01_genomic.fna/target_genomes.txt --output GCF_000347175.1_gls454194v01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:36,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:36,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:36,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:36,450] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:36,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:36,451] [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 alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	100.0	1410	1416	95	conclusive
Leptospira alexanderi	strain=L 60	GCA_000243815.3	100053	100053	type	True	83.7773	1036	1416	95	below_threshold
Leptospira santarosai	strain=LT 821	GCA_000313175.2	28183	28183	type	True	82.9633	969	1416	95	below_threshold
Leptospira kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	82.895	959	1416	95	below_threshold
Leptospira mayottensis	strain=200901116	GCA_000306675.3	1137606	1137606	type	True	82.766	998	1416	95	below_threshold
Leptospira borgpetersenii	strain=DSM 21538	GCA_003046425.1	174	174	type	True	82.6253	976	1416	95	below_threshold
Leptospira barantonii	strain=FH4-C-A1	GCA_002811925.1	2023184	2023184	type	True	82.4991	951	1416	95	below_threshold
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	81.7904	924	1416	95	below_threshold
Leptospira tipperaryensis	strain=GWTS #1	GCA_001729245.1	2564040	2564040	type	True	80.5853	817	1416	95	below_threshold
Leptospira adleri	strain=FH2-B-D1	GCA_002811985.1	2023186	2023186	type	True	80.5851	762	1416	95	below_threshold
Leptospira ainlahdjerensis	strain=201903070	GCA_016919175.1	2810033	2810033	type	True	80.3153	767	1416	95	below_threshold
Leptospira ellisii	strain=ATI7-C-A5	GCA_002811955.1	2023197	2023197	type	True	79.6246	582	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,453] [INFO] DFAST Taxonomy check result was written to GCF_000347175.1_gls454194v01_genomic.fna/tc_result.tsv
[2024-01-24 13:41:36,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:36,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:36,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference/checkm_data
[2024-01-24 13:41:36,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:36,509] [INFO] Task started: CheckM
[2024-01-24 13:41:36,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000347175.1_gls454194v01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000347175.1_gls454194v01_genomic.fna/checkm_input GCF_000347175.1_gls454194v01_genomic.fna/checkm_result
[2024-01-24 13:42:10,011] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:10,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:10,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:10,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000347175.1_gls454194v01_genomic.fna/markers.fasta)
[2024-01-24 13:42:10,036] [INFO] Task started: Blastn
[2024-01-24 13:42:10,036] [INFO] Running command: blastn -query GCF_000347175.1_gls454194v01_genomic.fna/markers.fasta -db /var/lib/cwl/stg32e68acb-8fef-4a28-b8ff-dfb43d259a17/dqc_reference/reference_markers_gtdb.fasta -out GCF_000347175.1_gls454194v01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:10,837] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:10,841] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:10,842] [INFO] Target genome list was writen to GCF_000347175.1_gls454194v01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:10,872] [INFO] Task started: fastANI
[2024-01-24 13:42:10,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg439fd421-c3bd-49ba-9f59-59a88b991984/GCF_000347175.1_gls454194v01_genomic.fna.gz --refList GCF_000347175.1_gls454194v01_genomic.fna/target_genomes_gtdb.txt --output GCF_000347175.1_gls454194v01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:23,435] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:23,448] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:23,449] [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_000347175.1	s__Leptospira alstonii	100.0	1410	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	conclusive
GCF_000332415.1	s__Leptospira weilii_A	91.381	1171	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243815.2	s__Leptospira alexanderi	83.8087	1032	1416	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	83.2966	1025	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	95.50	95.12	0.87	0.84	20	-
GCF_000313175.2	s__Leptospira santarosai	82.9874	964	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	98.62	96.47	0.92	0.90	43	-
GCF_000243735.2	s__Leptospira kmetyi	82.8962	957	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.04	98.99	0.96	0.94	7	-
GCF_003046425.1	s__Leptospira borgpetersenii	82.6453	973	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.13	97.82	0.96	0.92	148	-
GCF_002811925.1	s__Leptospira barantonii	82.496	952	1416	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	81.7859	924	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	97.33	95.78	0.94	0.93	8	-
GCF_002811985.1	s__Leptospira adleri	80.5977	761	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.11	98.26	0.94	0.91	3	-
GCF_001729245.1	s__Leptospira tipperaryensis	80.5618	821	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919175.1	s__Leptospira sp016919175	80.2739	773	1416	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:23,450] [INFO] GTDB search result was written to GCF_000347175.1_gls454194v01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:23,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:23,454] [INFO] DFAST_QC result json was written to GCF_000347175.1_gls454194v01_genomic.fna/dqc_result.json
[2024-01-24 13:42:23,454] [INFO] DFAST_QC completed!
[2024-01-24 13:42:23,454] [INFO] Total running time: 0h1m12s