[2024-01-24 12:42:09,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference
[2024-01-24 12:42:10,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,506] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ab5c699-7185-4fe2-832e-a26b2ce736bf/GCF_003114855.1_ASM311485v1_genomic.fna.gz | prodigal -d GCF_003114855.1_ASM311485v1_genomic.fna/cds.fna -a GCF_003114855.1_ASM311485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:20,109] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:20,110] [INFO] Task started: HMMsearch
[2024-01-24 12:42:20,110] [INFO] Running command: hmmsearch --tblout GCF_003114855.1_ASM311485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference/reference_markers.hmm GCF_003114855.1_ASM311485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:20,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:20,382] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4ab5c699-7185-4fe2-832e-a26b2ce736bf/GCF_003114855.1_ASM311485v1_genomic.fna.gz]
[2024-01-24 12:42:20,423] [INFO] Query marker FASTA was written to GCF_003114855.1_ASM311485v1_genomic.fna/markers.fasta
[2024-01-24 12:42:20,423] [INFO] Task started: Blastn
[2024-01-24 12:42:20,423] [INFO] Running command: blastn -query GCF_003114855.1_ASM311485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference/reference_markers.fasta -out GCF_003114855.1_ASM311485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:21,015] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:21,017] [INFO] Selected 18 target genomes.
[2024-01-24 12:42:21,018] [INFO] Target genome list was writen to GCF_003114855.1_ASM311485v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:21,026] [INFO] Task started: fastANI
[2024-01-24 12:42:21,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ab5c699-7185-4fe2-832e-a26b2ce736bf/GCF_003114855.1_ASM311485v1_genomic.fna.gz --refList GCF_003114855.1_ASM311485v1_genomic.fna/target_genomes.txt --output GCF_003114855.1_ASM311485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:32,430] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:32,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:32,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:32,443] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:32,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:32,444] [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 ryugenii	strain=YH101	GCA_003114855.1	1917863	1917863	type	True	100.0	1305	1305	95	conclusive
Leptospira ognonensis	strain=201702476	GCA_004770745.1	2484945	2484945	type	True	77.3648	197	1305	95	below_threshold
Leptospira meyeri	strain=DSM 21537	GCA_004368965.1	29508	29508	type	True	77.0057	170	1305	95	below_threshold
Leptospira levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	76.9722	178	1305	95	below_threshold
Leptospira abararensis	strain=201903074	GCA_016918735.1	2810036	2810036	type	True	76.9684	170	1305	95	below_threshold
Leptospira ilyithenensis	strain=201400974	GCA_004771005.1	2484901	2484901	type	True	76.8977	138	1305	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	76.8972	178	1305	95	below_threshold
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	76.7912	170	1305	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	76.7539	164	1305	95	below_threshold
Leptospira biflexa	strain=Patoc 1 (Paris)	GCA_000017685.1	172	172	type	True	76.6534	176	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:32,445] [INFO] DFAST Taxonomy check result was written to GCF_003114855.1_ASM311485v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:32,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:32,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:32,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference/checkm_data
[2024-01-24 12:42:32,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:32,486] [INFO] Task started: CheckM
[2024-01-24 12:42:32,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003114855.1_ASM311485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003114855.1_ASM311485v1_genomic.fna/checkm_input GCF_003114855.1_ASM311485v1_genomic.fna/checkm_result
[2024-01-24 12:43:05,669] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:05,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:05,694] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:05,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:05,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003114855.1_ASM311485v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:05,695] [INFO] Task started: Blastn
[2024-01-24 12:43:05,696] [INFO] Running command: blastn -query GCF_003114855.1_ASM311485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77ac6dc0-c553-4c04-9937-953783b4ce82/dqc_reference/reference_markers_gtdb.fasta -out GCF_003114855.1_ASM311485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:06,574] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:06,579] [INFO] Selected 20 target genomes.
[2024-01-24 12:43:06,579] [INFO] Target genome list was writen to GCF_003114855.1_ASM311485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:06,594] [INFO] Task started: fastANI
[2024-01-24 12:43:06,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ab5c699-7185-4fe2-832e-a26b2ce736bf/GCF_003114855.1_ASM311485v1_genomic.fna.gz --refList GCF_003114855.1_ASM311485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003114855.1_ASM311485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:19,000] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:19,018] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:19,019] [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_003114855.1	s__Leptospira_A ryugenii	100.0	1305	1305	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004769635.1	s__Leptospira_A jelokensis	77.1931	180	1305	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_004770995.1	s__Leptospira_A idonii	77.1552	153	1305	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_004770905.1	s__Leptospira_A bandrabouensis	77.0699	167	1305	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_004769525.1	s__Leptospira_A bouyouniensis	77.0606	181	1305	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_016918735.1	s__Leptospira_A sp016918735	76.9767	172	1305	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_016919165.1	s__Leptospira_A sp016919165	76.9109	176	1305	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_004769235.1	s__Leptospira_A kanakyensis	76.8964	182	1305	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_004770045.1	s__Leptospira_A montravelensis	76.8915	166	1305	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004769665.1	s__Leptospira_A kemamanensis	76.8273	179	1305	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	76.7928	159	1305	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_002811945.1	s__Leptospira_A harrisiae	76.7686	171	1305	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_002812125.1	s__Leptospira_A brenneri	76.7347	164	1305	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.47	99.47	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:19,021] [INFO] GTDB search result was written to GCF_003114855.1_ASM311485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:19,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:19,026] [INFO] DFAST_QC result json was written to GCF_003114855.1_ASM311485v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:19,026] [INFO] DFAST_QC completed!
[2024-01-24 12:43:19,026] [INFO] Total running time: 0h1m10s