[2024-01-25 18:07:35,857] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:35,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:35,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference
[2024-01-25 18:07:37,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:37,024] [INFO] Task started: Prodigal
[2024-01-25 18:07:37,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg26f662a4-8547-4ef2-835d-6d6fb73b3310/GCF_002811955.2_ASM281195v2_genomic.fna.gz | prodigal -d GCF_002811955.2_ASM281195v2_genomic.fna/cds.fna -a GCF_002811955.2_ASM281195v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:46,082] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:46,083] [INFO] Task started: HMMsearch
[2024-01-25 18:07:46,083] [INFO] Running command: hmmsearch --tblout GCF_002811955.2_ASM281195v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference/reference_markers.hmm GCF_002811955.2_ASM281195v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:46,319] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:46,320] [INFO] Found 6/6 markers.
[2024-01-25 18:07:46,355] [INFO] Query marker FASTA was written to GCF_002811955.2_ASM281195v2_genomic.fna/markers.fasta
[2024-01-25 18:07:46,355] [INFO] Task started: Blastn
[2024-01-25 18:07:46,355] [INFO] Running command: blastn -query GCF_002811955.2_ASM281195v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference/reference_markers.fasta -out GCF_002811955.2_ASM281195v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:46,890] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:46,893] [INFO] Selected 11 target genomes.
[2024-01-25 18:07:46,893] [INFO] Target genome list was writen to GCF_002811955.2_ASM281195v2_genomic.fna/target_genomes.txt
[2024-01-25 18:07:46,896] [INFO] Task started: fastANI
[2024-01-25 18:07:46,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f662a4-8547-4ef2-835d-6d6fb73b3310/GCF_002811955.2_ASM281195v2_genomic.fna.gz --refList GCF_002811955.2_ASM281195v2_genomic.fna/target_genomes.txt --output GCF_002811955.2_ASM281195v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:57,003] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:57,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:57,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:57,012] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:57,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:57,012] [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 ellisii	strain=ATI7-C-A5	GCA_002811955.1	2023197	2023197	type	True	99.7003	1118	1403	95	conclusive
Leptospira kmetyi	strain=Bejo-Iso9	GCA_000243735.3	408139	408139	type	True	80.6137	894	1403	95	below_threshold
Leptospira yasudae	strain=F1	GCA_003545925.1	2202201	2202201	type	True	80.5755	863	1403	95	below_threshold
Leptospira barantonii	strain=FH4-C-A1	GCA_002811925.1	2023184	2023184	type	True	80.2856	860	1403	95	below_threshold
Leptospira adleri	strain=FH2-B-D1	GCA_002811985.1	2023186	2023186	type	True	79.8851	737	1403	95	below_threshold
Leptospira alstonii	strain=79601	GCA_000347175.1	28452	28452	type	True	79.7515	679	1403	95	below_threshold
Leptospira ainazelensis	strain=201903071	GCA_016918785.1	2810034	2810034	type	True	79.735	747	1403	95	below_threshold
Leptospira interrogans	strain=ATCC 43642	GCA_900156205.1	173	173	type	True	78.4121	409	1403	95	below_threshold
Leptospira kirschneri	strain=3522 CT	GCA_000243695.3	29507	29507	type	True	78.3945	463	1403	95	below_threshold
Leptospira neocaledonica	strain=ES4-C-A1	GCA_002812205.1	2023192	2023192	type	True	76.0666	82	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:57,013] [INFO] DFAST Taxonomy check result was written to GCF_002811955.2_ASM281195v2_genomic.fna/tc_result.tsv
[2024-01-25 18:07:57,015] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:57,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:57,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference/checkm_data
[2024-01-25 18:07:57,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:57,059] [INFO] Task started: CheckM
[2024-01-25 18:07:57,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002811955.2_ASM281195v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002811955.2_ASM281195v2_genomic.fna/checkm_input GCF_002811955.2_ASM281195v2_genomic.fna/checkm_result
[2024-01-25 18:08:26,413] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:26,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:26,436] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:26,436] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:26,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002811955.2_ASM281195v2_genomic.fna/markers.fasta)
[2024-01-25 18:08:26,437] [INFO] Task started: Blastn
[2024-01-25 18:08:26,438] [INFO] Running command: blastn -query GCF_002811955.2_ASM281195v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a65611-bf10-44d2-9b12-0a1bee46944e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002811955.2_ASM281195v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:27,187] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:27,189] [INFO] Selected 7 target genomes.
[2024-01-25 18:08:27,189] [INFO] Target genome list was writen to GCF_002811955.2_ASM281195v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:27,196] [INFO] Task started: fastANI
[2024-01-25 18:08:27,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f662a4-8547-4ef2-835d-6d6fb73b3310/GCF_002811955.2_ASM281195v2_genomic.fna.gz --refList GCF_002811955.2_ASM281195v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002811955.2_ASM281195v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:33,850] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:33,856] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:33,856] [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_002811955.1	s__Leptospira ellisii	99.7003	1118	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004770155.1	s__Leptospira gomenensis	85.9407	1217	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.98	99.98	0.99	0.99	4	-
GCF_000243735.2	s__Leptospira kmetyi	80.6209	893	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.04	98.99	0.96	0.94	7	-
GCF_003545925.1	s__Leptospira yasudae	80.5825	862	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	97.33	95.78	0.94	0.93	8	-
GCF_002811925.1	s__Leptospira barantonii	80.2789	861	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	96.36	96.36	0.93	0.93	2	-
GCF_000332415.1	s__Leptospira weilii_A	79.7685	661	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347175.1	s__Leptospira alstonii	79.7514	679	1403	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira	95.0	99.79	99.25	0.97	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:33,858] [INFO] GTDB search result was written to GCF_002811955.2_ASM281195v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:33,859] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:33,864] [INFO] DFAST_QC result json was written to GCF_002811955.2_ASM281195v2_genomic.fna/dqc_result.json
[2024-01-25 18:08:33,864] [INFO] DFAST_QC completed!
[2024-01-25 18:08:33,864] [INFO] Total running time: 0h0m58s