[2024-01-24 13:40:34,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference
[2024-01-24 13:40:36,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,452] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,452] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4daa0d9-e097-4169-86e5-7dd1206b2c87/GCF_004770615.1_ASM477061v1_genomic.fna.gz | prodigal -d GCF_004770615.1_ASM477061v1_genomic.fna/cds.fna -a GCF_004770615.1_ASM477061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:46,183] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:46,184] [INFO] Task started: HMMsearch
[2024-01-24 13:40:46,184] [INFO] Running command: hmmsearch --tblout GCF_004770615.1_ASM477061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference/reference_markers.hmm GCF_004770615.1_ASM477061v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,551] [INFO] Found 6/6 markers.
[2024-01-24 13:40:46,589] [INFO] Query marker FASTA was written to GCF_004770615.1_ASM477061v1_genomic.fna/markers.fasta
[2024-01-24 13:40:46,590] [INFO] Task started: Blastn
[2024-01-24 13:40:46,590] [INFO] Running command: blastn -query GCF_004770615.1_ASM477061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference/reference_markers.fasta -out GCF_004770615.1_ASM477061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:47,226] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:47,229] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:47,229] [INFO] Target genome list was writen to GCF_004770615.1_ASM477061v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:47,235] [INFO] Task started: fastANI
[2024-01-24 13:40:47,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4daa0d9-e097-4169-86e5-7dd1206b2c87/GCF_004770615.1_ASM477061v1_genomic.fna.gz --refList GCF_004770615.1_ASM477061v1_genomic.fna/target_genomes.txt --output GCF_004770615.1_ASM477061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:56,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:56,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:56,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:56,795] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:56,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:56,795] [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 langatensis	strain=SSW18	GCA_004770615.1	2484983	2484983	type	True	100.0	1358	1358	95	conclusive
Leptospira semungkisensis	strain=SSS9	GCA_004770055.1	2484985	2484985	type	True	84.411	1138	1358	95	below_threshold
Leptospira johnsonii	strain=E8	GCA_003112675.1	1917820	1917820	type	True	79.6002	705	1358	95	below_threshold
Leptospira selangorensis	strain=SSW17	GCA_004769405.1	2484982	2484982	type	True	79.5376	702	1358	95	below_threshold
Leptospira licerasiae	strain=VAR 010	GCA_000244755.3	447106	447106	type	True	79.512	696	1358	95	below_threshold
Leptospira neocaledonica	strain=ES4-C-A1	GCA_002812205.1	2023192	2023192	type	True	79.4868	678	1358	95	below_threshold
Leptospira licerasiae	strain=ATCC BAA-1110	GCA_000526875.1	447106	447106	type	True	79.4839	699	1358	95	below_threshold
Leptospira hartskeerlii	strain=MCA2-B-A3	GCA_002811475.1	2023177	2023177	type	True	79.4077	707	1358	95	below_threshold
Leptospira saintgironsiae	strain=FH4-C-A2	GCA_002811765.1	2023183	2023183	type	True	79.4053	670	1358	95	below_threshold
Leptospira haakeii	strain=ATI7-C-A4	GCA_002812045.1	2023198	2023198	type	True	79.2898	664	1358	95	below_threshold
Leptospira wolffii	strain=Khorat-H2	GCA_000306115.2	409998	409998	type	True	78.9164	558	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,797] [INFO] DFAST Taxonomy check result was written to GCF_004770615.1_ASM477061v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:56,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:56,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:56,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference/checkm_data
[2024-01-24 13:40:56,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:56,839] [INFO] Task started: CheckM
[2024-01-24 13:40:56,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004770615.1_ASM477061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004770615.1_ASM477061v1_genomic.fna/checkm_input GCF_004770615.1_ASM477061v1_genomic.fna/checkm_result
[2024-01-24 13:41:32,242] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:32,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:32,268] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:32,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:32,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004770615.1_ASM477061v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:32,269] [INFO] Task started: Blastn
[2024-01-24 13:41:32,270] [INFO] Running command: blastn -query GCF_004770615.1_ASM477061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce3772e8-2b0c-4e93-9496-7dfd492d1907/dqc_reference/reference_markers_gtdb.fasta -out GCF_004770615.1_ASM477061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:33,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:33,117] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:33,117] [INFO] Target genome list was writen to GCF_004770615.1_ASM477061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:33,138] [INFO] Task started: fastANI
[2024-01-24 13:41:33,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4daa0d9-e097-4169-86e5-7dd1206b2c87/GCF_004770615.1_ASM477061v1_genomic.fna.gz --refList GCF_004770615.1_ASM477061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004770615.1_ASM477061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:45,217] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,230] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:45,231] [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_004770615.1	s__Leptospira_B langatensis	100.0	1358	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_004770055.1	s__Leptospira_B semungkisensis	84.4093	1139	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770895.1	s__Leptospira_B dzoumogneensis	79.658	719	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112675.1	s__Leptospira_B johnsonii	79.6159	702	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769405.1	s__Leptospira_B selangorensis	79.5405	701	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	97.97	97.97	0.98	0.97	3	-
GCF_000244755.1	s__Leptospira_B licerasiae	79.5114	696	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	99.34	97.39	0.98	0.94	5	-
GCF_002812205.1	s__Leptospira_B neocaledonica	79.4772	679	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770105.1	s__Leptospira_B andrefontaineae	79.4635	680	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811475.1	s__Leptospira_B hartskeerlii	79.4061	707	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002811765.1	s__Leptospira_B saintgironsiae	79.3989	670	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347035.1	s__Leptospira_B sp000347035	79.3886	669	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769555.1	s__Leptospira_B koniambonensis	79.3169	676	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812045.1	s__Leptospira_B haakeii	79.2996	663	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000306115.2	s__Leptospira_B wolffii	78.9063	556	1358	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	96.66	96.35	0.96	0.95	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,232] [INFO] GTDB search result was written to GCF_004770615.1_ASM477061v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:45,233] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:45,236] [INFO] DFAST_QC result json was written to GCF_004770615.1_ASM477061v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:45,237] [INFO] DFAST_QC completed!
[2024-01-24 13:41:45,237] [INFO] Total running time: 0h1m10s