[2024-01-24 12:47:12,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference
[2024-01-24 12:47:13,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,651] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,652] [INFO] Running command: gunzip -c /var/lib/cwl/stge097eb9b-658b-452d-99b0-a68392a28c62/GCF_000306115.2_gls454061v02_genomic.fna.gz | prodigal -d GCF_000306115.2_gls454061v02_genomic.fna/cds.fna -a GCF_000306115.2_gls454061v02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:24,267] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:24,267] [INFO] Task started: HMMsearch
[2024-01-24 12:47:24,267] [INFO] Running command: hmmsearch --tblout GCF_000306115.2_gls454061v02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference/reference_markers.hmm GCF_000306115.2_gls454061v02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:24,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:24,590] [INFO] Found 6/6 markers.
[2024-01-24 12:47:24,637] [INFO] Query marker FASTA was written to GCF_000306115.2_gls454061v02_genomic.fna/markers.fasta
[2024-01-24 12:47:24,638] [INFO] Task started: Blastn
[2024-01-24 12:47:24,638] [INFO] Running command: blastn -query GCF_000306115.2_gls454061v02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference/reference_markers.fasta -out GCF_000306115.2_gls454061v02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:25,323] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:25,326] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:25,326] [INFO] Target genome list was writen to GCF_000306115.2_gls454061v02_genomic.fna/target_genomes.txt
[2024-01-24 12:47:25,335] [INFO] Task started: fastANI
[2024-01-24 12:47:25,336] [INFO] Running command: fastANI --query /var/lib/cwl/stge097eb9b-658b-452d-99b0-a68392a28c62/GCF_000306115.2_gls454061v02_genomic.fna.gz --refList GCF_000306115.2_gls454061v02_genomic.fna/target_genomes.txt --output GCF_000306115.2_gls454061v02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:37,826] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:37,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:37,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:37,840] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:37,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:37,841] [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 wolffii	strain=Khorat-H2	GCA_000306115.2	409998	409998	type	True	100.0	1452	1455	95	conclusive
Leptospira licerasiae	strain=VAR 010	GCA_000244755.3	447106	447106	type	True	78.9498	541	1455	95	below_threshold
Leptospira licerasiae	strain=ATCC BAA-1110	GCA_000526875.1	447106	447106	type	True	78.8382	537	1455	95	below_threshold
Leptospira semungkisensis	strain=SSS9	GCA_004770055.1	2484985	2484985	type	True	78.8039	552	1455	95	below_threshold
Leptospira langatensis	strain=SSW18	GCA_004770615.1	2484983	2484983	type	True	78.801	559	1455	95	below_threshold
Leptospira johnsonii	strain=E8	GCA_003112675.1	1917820	1917820	type	True	78.7735	534	1455	95	below_threshold
Leptospira hartskeerlii	strain=MCA2-B-A3	GCA_002811475.1	2023177	2023177	type	True	78.7332	513	1455	95	below_threshold
Leptospira venezuelensis	strain=CLM-U50	GCA_002150035.1	1958811	1958811	type	True	78.6696	483	1455	95	below_threshold
Leptospira saintgironsiae	strain=FH4-C-A2	GCA_002811765.1	2023183	2023183	type	True	78.6315	474	1455	95	below_threshold
Leptospira neocaledonica	strain=ES4-C-A1	GCA_002812205.1	2023192	2023192	type	True	78.6274	536	1455	95	below_threshold
Leptospira inadai	strain=10	GCA_000243675.3	29506	29506	type	True	77.7615	261	1455	95	below_threshold
Leptospira broomii	strain=5399	GCA_000243715.3	301541	301541	type	True	77.6231	249	1455	95	below_threshold
Leptospira fletcheri	strain=SSW15	GCA_004769195.1	2484981	2484981	type	True	77.4	322	1455	95	below_threshold
Leptospira kirschneri	strain=3522 CT	GCA_000243695.3	29507	29507	type	True	76.8897	87	1455	95	below_threshold
Leptospira tipperaryensis	strain=GWTS #1	GCA_001729245.1	2564040	2564040	type	True	76.5645	141	1455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:37,843] [INFO] DFAST Taxonomy check result was written to GCF_000306115.2_gls454061v02_genomic.fna/tc_result.tsv
[2024-01-24 12:47:37,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:37,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:37,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference/checkm_data
[2024-01-24 12:47:37,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:37,888] [INFO] Task started: CheckM
[2024-01-24 12:47:37,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000306115.2_gls454061v02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000306115.2_gls454061v02_genomic.fna/checkm_input GCF_000306115.2_gls454061v02_genomic.fna/checkm_result
[2024-01-24 12:48:12,394] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:12,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:12,416] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:12,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:12,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000306115.2_gls454061v02_genomic.fna/markers.fasta)
[2024-01-24 12:48:12,417] [INFO] Task started: Blastn
[2024-01-24 12:48:12,417] [INFO] Running command: blastn -query GCF_000306115.2_gls454061v02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b223cc-285f-4881-9693-0a70849519a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000306115.2_gls454061v02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:13,223] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:13,227] [INFO] Selected 16 target genomes.
[2024-01-24 12:48:13,227] [INFO] Target genome list was writen to GCF_000306115.2_gls454061v02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:13,239] [INFO] Task started: fastANI
[2024-01-24 12:48:13,239] [INFO] Running command: fastANI --query /var/lib/cwl/stge097eb9b-658b-452d-99b0-a68392a28c62/GCF_000306115.2_gls454061v02_genomic.fna.gz --refList GCF_000306115.2_gls454061v02_genomic.fna/target_genomes_gtdb.txt --output GCF_000306115.2_gls454061v02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:26,373] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:26,397] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:26,398] [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_000306115.2	s__Leptospira_B wolffii	100.0	1452	1455	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	96.66	96.35	0.96	0.95	7	conclusive
GCF_000347035.1	s__Leptospira_B sp000347035	78.9487	535	1455	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_000244755.1	s__Leptospira_B licerasiae	78.9202	543	1455	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_004770105.1	s__Leptospira_B andrefontaineae	78.8146	484	1455	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_004770055.1	s__Leptospira_B semungkisensis	78.8039	552	1455	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_004770615.1	s__Leptospira_B langatensis	78.801	559	1455	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004769615.1	s__Leptospira_B sarikeiensis	78.7728	546	1455	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	78.7674	534	1455	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	78.7438	585	1455	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	78.7305	512	1455	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_002150035.1	s__Leptospira_B venezuelensis	78.6506	483	1455	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002811765.1	s__Leptospira_B saintgironsiae	78.6224	474	1455	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_002812205.1	s__Leptospira_B neocaledonica	78.6171	538	1455	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_000243675.2	s__Leptospira_B inadai	77.7371	259	1455	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000243715.2	s__Leptospira_B broomii	77.6223	249	1455	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_004769195.1	s__Leptospira_B fletcheri	77.4015	321	1455	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:26,399] [INFO] GTDB search result was written to GCF_000306115.2_gls454061v02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:26,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:26,405] [INFO] DFAST_QC result json was written to GCF_000306115.2_gls454061v02_genomic.fna/dqc_result.json
[2024-01-24 12:48:26,405] [INFO] DFAST_QC completed!
[2024-01-24 12:48:26,405] [INFO] Total running time: 0h1m14s