[2024-01-24 13:28:01,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference
[2024-01-24 13:28:03,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,489] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,489] [INFO] Running command: gunzip -c /var/lib/cwl/stg60d96fbb-9306-4804-b2b3-dae1f97161fc/GCF_000332495.1_gls454203v02_genomic.fna.gz | prodigal -d GCF_000332495.1_gls454203v02_genomic.fna/cds.fna -a GCF_000332495.1_gls454203v02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:12,920] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:12,921] [INFO] Task started: HMMsearch
[2024-01-24 13:28:12,921] [INFO] Running command: hmmsearch --tblout GCF_000332495.1_gls454203v02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference/reference_markers.hmm GCF_000332495.1_gls454203v02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,190] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,226] [INFO] Query marker FASTA was written to GCF_000332495.1_gls454203v02_genomic.fna/markers.fasta
[2024-01-24 13:28:13,226] [INFO] Task started: Blastn
[2024-01-24 13:28:13,226] [INFO] Running command: blastn -query GCF_000332495.1_gls454203v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference/reference_markers.fasta -out GCF_000332495.1_gls454203v02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:13,830] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:13,833] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:13,833] [INFO] Target genome list was writen to GCF_000332495.1_gls454203v02_genomic.fna/target_genomes.txt
[2024-01-24 13:28:13,838] [INFO] Task started: fastANI
[2024-01-24 13:28:13,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d96fbb-9306-4804-b2b3-dae1f97161fc/GCF_000332495.1_gls454203v02_genomic.fna.gz --refList GCF_000332495.1_gls454203v02_genomic.fna/target_genomes.txt --output GCF_000332495.1_gls454203v02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:23,634] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:23,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:23,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:23,644] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:23,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:23,645] [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 terpstrae	strain=LT 11-33	GCA_000332495.2	293075	293075	type	True	100.0	1352	1353	95	conclusive
Leptospira abararensis	strain=201903074	GCA_016918735.1	2810036	2810036	type	True	86.9639	1162	1353	95	below_threshold
Leptospira vanthielii	strain=Waz Holland	GCA_000332455.2	293085	293085	type	True	86.4843	1115	1353	95	below_threshold
Leptospira wolbachii	strain=CDC	GCA_000332515.2	29511	29511	type	True	86.2049	1138	1353	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	85.1084	1091	1353	95	below_threshold
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	83.5875	1055	1353	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	83.3578	1032	1353	95	below_threshold
Leptospira meyeri	strain=DSM 21537	GCA_004368965.1	29508	29508	type	True	83.2241	1037	1353	95	below_threshold
Leptospira levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	80.9836	791	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:23,647] [INFO] DFAST Taxonomy check result was written to GCF_000332495.1_gls454203v02_genomic.fna/tc_result.tsv
[2024-01-24 13:28:23,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:23,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:23,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference/checkm_data
[2024-01-24 13:28:23,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:23,689] [INFO] Task started: CheckM
[2024-01-24 13:28:23,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000332495.1_gls454203v02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000332495.1_gls454203v02_genomic.fna/checkm_input GCF_000332495.1_gls454203v02_genomic.fna/checkm_result
[2024-01-24 13:28:56,959] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:56,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,977] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:56,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:56,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000332495.1_gls454203v02_genomic.fna/markers.fasta)
[2024-01-24 13:28:56,978] [INFO] Task started: Blastn
[2024-01-24 13:28:56,978] [INFO] Running command: blastn -query GCF_000332495.1_gls454203v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg147b167e-7e2c-48d0-b4b3-6610b22c4ace/dqc_reference/reference_markers_gtdb.fasta -out GCF_000332495.1_gls454203v02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:57,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:57,746] [INFO] Selected 8 target genomes.
[2024-01-24 13:28:57,746] [INFO] Target genome list was writen to GCF_000332495.1_gls454203v02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:57,758] [INFO] Task started: fastANI
[2024-01-24 13:28:57,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d96fbb-9306-4804-b2b3-dae1f97161fc/GCF_000332495.1_gls454203v02_genomic.fna.gz --refList GCF_000332495.1_gls454203v02_genomic.fna/target_genomes_gtdb.txt --output GCF_000332495.1_gls454203v02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:06,185] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:06,192] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:06,193] [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_000332495.1	s__Leptospira_A terpstrae	100.0	1352	1353	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_016918735.1	s__Leptospira_A sp016918735	86.9663	1162	1353	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_000332455.1	s__Leptospira_A vanthielii	86.5002	1112	1353	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.49	98.49	0.94	0.94	2	-
GCF_000332515.2	s__Leptospira_A wolbachii	86.2019	1139	1353	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	85.0997	1093	1353	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	83.6875	1077	1353	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	83.5876	1055	1353	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	83.371	1030	1353	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 13:29:06,195] [INFO] GTDB search result was written to GCF_000332495.1_gls454203v02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:06,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:06,198] [INFO] DFAST_QC result json was written to GCF_000332495.1_gls454203v02_genomic.fna/dqc_result.json
[2024-01-24 13:29:06,199] [INFO] DFAST_QC completed!
[2024-01-24 13:29:06,199] [INFO] Total running time: 0h1m4s