[2024-01-24 13:09:49,439] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference
[2024-01-24 13:09:50,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,776] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,776] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4f7ef3f-387e-4d6d-8871-a7e7275dd4b5/GCF_004770745.1_ASM477074v1_genomic.fna.gz | prodigal -d GCF_004770745.1_ASM477074v1_genomic.fna/cds.fna -a GCF_004770745.1_ASM477074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:59,993] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:59,994] [INFO] Task started: HMMsearch
[2024-01-24 13:09:59,994] [INFO] Running command: hmmsearch --tblout GCF_004770745.1_ASM477074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference/reference_markers.hmm GCF_004770745.1_ASM477074v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:00,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:00,280] [INFO] Found 6/6 markers.
[2024-01-24 13:10:00,315] [INFO] Query marker FASTA was written to GCF_004770745.1_ASM477074v1_genomic.fna/markers.fasta
[2024-01-24 13:10:00,315] [INFO] Task started: Blastn
[2024-01-24 13:10:00,315] [INFO] Running command: blastn -query GCF_004770745.1_ASM477074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference/reference_markers.fasta -out GCF_004770745.1_ASM477074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:00,887] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:00,891] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:00,891] [INFO] Target genome list was writen to GCF_004770745.1_ASM477074v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:00,915] [INFO] Task started: fastANI
[2024-01-24 13:10:00,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f7ef3f-387e-4d6d-8871-a7e7275dd4b5/GCF_004770745.1_ASM477074v1_genomic.fna.gz --refList GCF_004770745.1_ASM477074v1_genomic.fna/target_genomes.txt --output GCF_004770745.1_ASM477074v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:10,771] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:10,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:10,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:10,783] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:10,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:10,784] [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 ognonensis	strain=201702476	GCA_004770745.1	2484945	2484945	type	True	100.0	1299	1299	95	conclusive
Leptospira meyeri	strain=DSM 21537	GCA_004368965.1	29508	29508	type	True	77.5195	182	1299	95	below_threshold
Leptospira ryugenii	strain=YH101	GCA_003114855.1	1917863	1917863	type	True	77.4537	191	1299	95	below_threshold
Leptospira kobayashii	strain=E30	GCA_003114835.3	1917830	1917830	type	True	77.3632	202	1299	95	below_threshold
Leptospira ilyithenensis	strain=201400974	GCA_004771005.1	2484901	2484901	type	True	77.2847	194	1299	95	below_threshold
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	77.2023	183	1299	95	below_threshold
Leptospira ellinghausenii	strain=E18	GCA_003114815.1	1917822	1917822	type	True	77.1794	184	1299	95	below_threshold
Leptospira terpstrae	strain=LT 11-33	GCA_000332495.2	293075	293075	type	True	77.115	207	1299	95	below_threshold
Leptospira yanagawae	strain=Sao Paulo	GCA_000332475.2	293069	293069	type	True	77.042	187	1299	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	76.9288	187	1299	95	below_threshold
Leptospira levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	76.9192	200	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:10,786] [INFO] DFAST Taxonomy check result was written to GCF_004770745.1_ASM477074v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:10,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:10,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:10,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference/checkm_data
[2024-01-24 13:10:10,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:10,835] [INFO] Task started: CheckM
[2024-01-24 13:10:10,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004770745.1_ASM477074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004770745.1_ASM477074v1_genomic.fna/checkm_input GCF_004770745.1_ASM477074v1_genomic.fna/checkm_result
[2024-01-24 13:10:42,626] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:42,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:42,646] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:42,646] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:42,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004770745.1_ASM477074v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:42,647] [INFO] Task started: Blastn
[2024-01-24 13:10:42,647] [INFO] Running command: blastn -query GCF_004770745.1_ASM477074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb40bd899-8ac2-4098-941b-9b8594d4bb9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004770745.1_ASM477074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:43,353] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:43,357] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:43,357] [INFO] Target genome list was writen to GCF_004770745.1_ASM477074v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:43,542] [INFO] Task started: fastANI
[2024-01-24 13:10:43,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f7ef3f-387e-4d6d-8871-a7e7275dd4b5/GCF_004770745.1_ASM477074v1_genomic.fna.gz --refList GCF_004770745.1_ASM477074v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004770745.1_ASM477074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:54,400] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:54,415] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:54,416] [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_004770745.1	s__Leptospira_A ognonensis	100.0	1299	1299	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_003114835.1	s__Leptospira_A kobayashii	77.3756	198	1299	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_004770475.1	s__Leptospira_A mtsangambouensis	77.315	202	1299	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_004771005.1	s__Leptospira_A ilyithenensis	77.2701	195	1299	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	77.2316	205	1299	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_003114815.1	s__Leptospira_A ellinghausenii	77.1646	183	1299	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_004770995.1	s__Leptospira_A idonii	77.1256	216	1299	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_004770265.1	s__Leptospira_A congkakensis	77.1163	193	1299	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_004770045.1	s__Leptospira_A montravelensis	77.0915	198	1299	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_000332475.2	s__Leptospira_A yanagawae	77.0606	188	1299	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.50	98.50	0.93	0.93	2	-
GCA_016742255.1	s__Leptospira_A sp016742255	77.0501	184	1299	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	76.9828	188	1299	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_004770765.1	s__Leptospira_A noumeaensis	76.9752	190	1299	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_004769635.1	s__Leptospira_A jelokensis	76.9467	185	1299	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_004769235.1	s__Leptospira_A kanakyensis	76.9241	213	1299	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_004769525.1	s__Leptospira_A bouyouniensis	76.9233	202	1299	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_002812085.1	s__Leptospira_A levettii	76.9192	200	1299	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.63	98.25	0.94	0.91	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:54,417] [INFO] GTDB search result was written to GCF_004770745.1_ASM477074v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:54,418] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:54,421] [INFO] DFAST_QC result json was written to GCF_004770745.1_ASM477074v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:54,421] [INFO] DFAST_QC completed!
[2024-01-24 13:10:54,421] [INFO] Total running time: 0h1m5s