[2023-06-18 21:21:19,947] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:21:19,953] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:21:19,953] [INFO] DQC Reference Directory: /var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference
[2023-06-18 21:21:21,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:21:21,498] [INFO] Task started: Prodigal
[2023-06-18 21:21:21,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg20e47430-4e8f-479c-9d7a-024056a96f12/GCA_018606705.1_ASM1860670v1_genomic.fna.gz | prodigal -d GCA_018606705.1_ASM1860670v1_genomic.fna/cds.fna -a GCA_018606705.1_ASM1860670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:21:28,568] [INFO] Task succeeded: Prodigal
[2023-06-18 21:21:28,569] [INFO] Task started: HMMsearch
[2023-06-18 21:21:28,569] [INFO] Running command: hmmsearch --tblout GCA_018606705.1_ASM1860670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference/reference_markers.hmm GCA_018606705.1_ASM1860670v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:21:28,906] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:21:28,907] [INFO] Found 6/6 markers.
[2023-06-18 21:21:28,960] [INFO] Query marker FASTA was written to GCA_018606705.1_ASM1860670v1_genomic.fna/markers.fasta
[2023-06-18 21:21:28,961] [INFO] Task started: Blastn
[2023-06-18 21:21:28,961] [INFO] Running command: blastn -query GCA_018606705.1_ASM1860670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference/reference_markers.fasta -out GCA_018606705.1_ASM1860670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:21:29,590] [INFO] Task succeeded: Blastn
[2023-06-18 21:21:29,598] [INFO] Selected 20 target genomes.
[2023-06-18 21:21:29,598] [INFO] Target genome list was writen to GCA_018606705.1_ASM1860670v1_genomic.fna/target_genomes.txt
[2023-06-18 21:21:29,602] [INFO] Task started: fastANI
[2023-06-18 21:21:29,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg20e47430-4e8f-479c-9d7a-024056a96f12/GCA_018606705.1_ASM1860670v1_genomic.fna.gz --refList GCA_018606705.1_ASM1860670v1_genomic.fna/target_genomes.txt --output GCA_018606705.1_ASM1860670v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:21:46,173] [INFO] Task succeeded: fastANI
[2023-06-18 21:21:46,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:21:46,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:21:46,182] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 21:21:46,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 21:21:46,183] [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 levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	98.1796	875	1002	95	conclusive
Leptospira ellinghausenii	strain=E18	GCA_003114815.1	1917822	1917822	type	True	92.1185	897	1002	95	below_threshold
Leptospira biflexa	strain=Patoc 1 (Paris)	GCA_000017685.1	172	172	type	True	82.8668	705	1002	95	below_threshold
Leptospira yanagawae	strain=Sao Paulo	GCA_000332475.2	293069	293069	type	True	82.4942	687	1002	95	below_threshold
Leptospira meyeri	strain=DSM 21537	GCA_004368965.1	29508	29508	type	True	80.558	561	1002	95	below_threshold
Leptospira harrisiae	strain=FH2-B-A1	GCA_002811945.1	2023189	2023189	type	True	80.3635	559	1002	95	below_threshold
Leptospira abararensis	strain=201903074	GCA_016918735.1	2810036	2810036	type	True	80.3585	530	1002	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	80.2355	528	1002	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	80.2246	550	1002	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:21:46,185] [INFO] DFAST Taxonomy check result was written to GCA_018606705.1_ASM1860670v1_genomic.fna/tc_result.tsv
[2023-06-18 21:21:46,186] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:21:46,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:21:46,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference/checkm_data
[2023-06-18 21:21:46,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:21:46,226] [INFO] Task started: CheckM
[2023-06-18 21:21:46,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018606705.1_ASM1860670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018606705.1_ASM1860670v1_genomic.fna/checkm_input GCA_018606705.1_ASM1860670v1_genomic.fna/checkm_result
[2023-06-18 21:22:14,586] [INFO] Task succeeded: CheckM
[2023-06-18 21:22:14,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.21%
Contamintation: 4.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:22:14,616] [INFO] ===== Completeness check finished =====
[2023-06-18 21:22:14,617] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:22:14,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018606705.1_ASM1860670v1_genomic.fna/markers.fasta)
[2023-06-18 21:22:14,618] [INFO] Task started: Blastn
[2023-06-18 21:22:14,618] [INFO] Running command: blastn -query GCA_018606705.1_ASM1860670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5745187e-c908-449f-947d-90d4d48f42f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018606705.1_ASM1860670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:22:15,391] [INFO] Task succeeded: Blastn
[2023-06-18 21:22:15,396] [INFO] Selected 18 target genomes.
[2023-06-18 21:22:15,397] [INFO] Target genome list was writen to GCA_018606705.1_ASM1860670v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:22:15,407] [INFO] Task started: fastANI
[2023-06-18 21:22:15,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg20e47430-4e8f-479c-9d7a-024056a96f12/GCA_018606705.1_ASM1860670v1_genomic.fna.gz --refList GCA_018606705.1_ASM1860670v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018606705.1_ASM1860670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:22:28,830] [INFO] Task succeeded: fastANI
[2023-06-18 21:22:28,841] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:22:28,841] [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_002812085.1	s__Leptospira_A levettii	98.1796	875	1002	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.63	98.25	0.94	0.91	14	conclusive
GCF_003114815.1	s__Leptospira_A ellinghausenii	92.1185	897	1002	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742255.1	s__Leptospira_A sp016742255	91.6741	846	1002	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_004769665.1	s__Leptospira_A kemamanensis	83.7983	696	1002	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_004769525.1	s__Leptospira_A bouyouniensis	83.0554	740	1002	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_000017685.1	s__Leptospira_A biflexa	82.8693	705	1002	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.66	98.34	0.97	0.95	7	-
GCF_000332475.2	s__Leptospira_A yanagawae	82.5055	686	1002	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.50	98.50	0.93	0.93	2	-
GCF_004770905.1	s__Leptospira_A bandrabouensis	80.4231	564	1002	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-18 21:22:28,844] [INFO] GTDB search result was written to GCA_018606705.1_ASM1860670v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:22:28,844] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:22:28,848] [INFO] DFAST_QC result json was written to GCA_018606705.1_ASM1860670v1_genomic.fna/dqc_result.json
[2023-06-18 21:22:28,848] [INFO] DFAST_QC completed!
[2023-06-18 21:22:28,848] [INFO] Total running time: 0h1m9s