[2024-01-24 14:14:46,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:46,981] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:46,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference
[2024-01-24 14:14:49,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,424] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcc7cf3f-35ed-4a9d-a3bf-86d98d8531d1/GCF_004368965.1_ASM436896v1_genomic.fna.gz | prodigal -d GCF_004368965.1_ASM436896v1_genomic.fna/cds.fna -a GCF_004368965.1_ASM436896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:00,394] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:00,394] [INFO] Task started: HMMsearch
[2024-01-24 14:15:00,394] [INFO] Running command: hmmsearch --tblout GCF_004368965.1_ASM436896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference/reference_markers.hmm GCF_004368965.1_ASM436896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:00,690] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:00,691] [INFO] Found 6/6 markers.
[2024-01-24 14:15:00,729] [INFO] Query marker FASTA was written to GCF_004368965.1_ASM436896v1_genomic.fna/markers.fasta
[2024-01-24 14:15:00,730] [INFO] Task started: Blastn
[2024-01-24 14:15:00,730] [INFO] Running command: blastn -query GCF_004368965.1_ASM436896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference/reference_markers.fasta -out GCF_004368965.1_ASM436896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:01,338] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:01,342] [INFO] Selected 9 target genomes.
[2024-01-24 14:15:01,342] [INFO] Target genome list was writen to GCF_004368965.1_ASM436896v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:01,347] [INFO] Task started: fastANI
[2024-01-24 14:15:01,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc7cf3f-35ed-4a9d-a3bf-86d98d8531d1/GCF_004368965.1_ASM436896v1_genomic.fna.gz --refList GCF_004368965.1_ASM436896v1_genomic.fna/target_genomes.txt --output GCF_004368965.1_ASM436896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:12,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:12,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:12,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:12,589] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:12,589] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:12,589] [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 meyeri	strain=DSM 21537	GCA_004368965.1	29508	29508	type	True	100.0	1406	1406	95	conclusive
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	85.909	1153	1406	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	83.4887	1008	1406	95	below_threshold
Leptospira wolbachii	strain=CDC	GCA_000332515.2	29511	29511	type	True	83.4149	1065	1406	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	83.3496	1047	1406	95	below_threshold
Leptospira abararensis	strain=201903074	GCA_016918735.1	2810036	2810036	type	True	83.316	1048	1406	95	below_threshold
Leptospira vanthielii	strain=Waz Holland	GCA_000332455.2	293085	293085	type	True	83.2334	1051	1406	95	below_threshold
Leptospira terpstrae	strain=LT 11-33	GCA_000332495.2	293075	293075	type	True	83.162	1064	1406	95	below_threshold
Leptospira yanagawae	strain=Sao Paulo	GCA_000332475.2	293069	293069	type	True	81.0603	763	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,591] [INFO] DFAST Taxonomy check result was written to GCF_004368965.1_ASM436896v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:12,591] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:12,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:12,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference/checkm_data
[2024-01-24 14:15:12,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:12,634] [INFO] Task started: CheckM
[2024-01-24 14:15:12,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004368965.1_ASM436896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004368965.1_ASM436896v1_genomic.fna/checkm_input GCF_004368965.1_ASM436896v1_genomic.fna/checkm_result
[2024-01-24 14:15:47,737] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:47,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:47,760] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:47,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:47,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004368965.1_ASM436896v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:47,761] [INFO] Task started: Blastn
[2024-01-24 14:15:47,761] [INFO] Running command: blastn -query GCF_004368965.1_ASM436896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11363473-0fea-4c5f-ba81-20d14ab4eb53/dqc_reference/reference_markers_gtdb.fasta -out GCF_004368965.1_ASM436896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:48,514] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:48,518] [INFO] Selected 10 target genomes.
[2024-01-24 14:15:48,519] [INFO] Target genome list was writen to GCF_004368965.1_ASM436896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:48,533] [INFO] Task started: fastANI
[2024-01-24 14:15:48,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc7cf3f-35ed-4a9d-a3bf-86d98d8531d1/GCF_004368965.1_ASM436896v1_genomic.fna.gz --refList GCF_004368965.1_ASM436896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004368965.1_ASM436896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:58,876] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:58,886] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:58,886] [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_004368965.1	s__Leptospira_A meyeri	100.0	1406	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	97.24	96.32	0.97	0.95	11	conclusive
GCF_004770475.1	s__Leptospira_A mtsangambouensis	89.4479	1244	1406	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_004770145.1	s__Leptospira_A bourretii	89.317	1247	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.12	99.11	0.96	0.96	4	-
GCF_002811945.1	s__Leptospira_A harrisiae	85.8919	1154	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.94	99.94	0.99	0.99	2	-
GCF_004770265.1	s__Leptospira_A congkakensis	85.083	1062	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.99	99.99	1.00	1.00	3	-
GCF_004770905.1	s__Leptospira_A bandrabouensis	84.7267	1053	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.97	99.97	0.99	0.99	2	-
GCF_004769235.1	s__Leptospira_A kanakyensis	84.5378	1070	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004770765.1	s__Leptospira_A noumeaensis	84.4136	1052	1406	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_004769575.1	s__Leptospira_A perdikensis	84.3063	1033	1406	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_004770045.1	s__Leptospira_A montravelensis	84.2324	1061	1406	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:58,891] [INFO] GTDB search result was written to GCF_004368965.1_ASM436896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:58,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:58,894] [INFO] DFAST_QC result json was written to GCF_004368965.1_ASM436896v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:58,895] [INFO] DFAST_QC completed!
[2024-01-24 14:15:58,895] [INFO] Total running time: 0h1m12s