[2023-06-30 14:10:44,742] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:10:44,745] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:10:44,745] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference
[2023-06-30 14:10:46,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:10:46,180] [INFO] Task started: Prodigal
[2023-06-30 14:10:46,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f9a79f0-e103-41db-a113-0960b42232c5/GCA_016708435.1_ASM1670843v1_genomic.fna.gz | prodigal -d GCA_016708435.1_ASM1670843v1_genomic.fna/cds.fna -a GCA_016708435.1_ASM1670843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:10:58,237] [INFO] Task succeeded: Prodigal
[2023-06-30 14:10:58,238] [INFO] Task started: HMMsearch
[2023-06-30 14:10:58,238] [INFO] Running command: hmmsearch --tblout GCA_016708435.1_ASM1670843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference/reference_markers.hmm GCA_016708435.1_ASM1670843v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:10:58,597] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:10:58,598] [INFO] Found 6/6 markers.
[2023-06-30 14:10:58,656] [INFO] Query marker FASTA was written to GCA_016708435.1_ASM1670843v1_genomic.fna/markers.fasta
[2023-06-30 14:10:58,660] [INFO] Task started: Blastn
[2023-06-30 14:10:58,660] [INFO] Running command: blastn -query GCA_016708435.1_ASM1670843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference/reference_markers.fasta -out GCA_016708435.1_ASM1670843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:10:59,253] [INFO] Task succeeded: Blastn
[2023-06-30 14:10:59,258] [INFO] Selected 25 target genomes.
[2023-06-30 14:10:59,258] [INFO] Target genome list was writen to GCA_016708435.1_ASM1670843v1_genomic.fna/target_genomes.txt
[2023-06-30 14:10:59,264] [INFO] Task started: fastANI
[2023-06-30 14:10:59,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f9a79f0-e103-41db-a113-0960b42232c5/GCA_016708435.1_ASM1670843v1_genomic.fna.gz --refList GCA_016708435.1_ASM1670843v1_genomic.fna/target_genomes.txt --output GCA_016708435.1_ASM1670843v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:11:13,197] [INFO] Task succeeded: fastANI
[2023-06-30 14:11:13,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:11:13,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:11:13,202] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:11:13,203] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:11:13,203] [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 wolbachii	strain=CDC	GCA_000332515.2	29511	29511	type	True	76.4211	50	2027	95	below_threshold
Leptospira terpstrae	strain=LT 11-33	GCA_000332495.2	293075	293075	type	True	76.1409	50	2027	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:11:13,205] [INFO] DFAST Taxonomy check result was written to GCA_016708435.1_ASM1670843v1_genomic.fna/tc_result.tsv
[2023-06-30 14:11:13,206] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:11:13,206] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:11:13,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference/checkm_data
[2023-06-30 14:11:13,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:11:13,266] [INFO] Task started: CheckM
[2023-06-30 14:11:13,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708435.1_ASM1670843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708435.1_ASM1670843v1_genomic.fna/checkm_input GCA_016708435.1_ASM1670843v1_genomic.fna/checkm_result
[2023-06-30 14:11:52,714] [INFO] Task succeeded: CheckM
[2023-06-30 14:11:52,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:11:52,741] [INFO] ===== Completeness check finished =====
[2023-06-30 14:11:52,741] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:11:52,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708435.1_ASM1670843v1_genomic.fna/markers.fasta)
[2023-06-30 14:11:52,742] [INFO] Task started: Blastn
[2023-06-30 14:11:52,742] [INFO] Running command: blastn -query GCA_016708435.1_ASM1670843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc58e1cf-907a-4350-9db4-116b2d4fb3e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708435.1_ASM1670843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:11:53,498] [INFO] Task succeeded: Blastn
[2023-06-30 14:11:53,501] [INFO] Selected 11 target genomes.
[2023-06-30 14:11:53,502] [INFO] Target genome list was writen to GCA_016708435.1_ASM1670843v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:11:53,506] [INFO] Task started: fastANI
[2023-06-30 14:11:53,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f9a79f0-e103-41db-a113-0960b42232c5/GCA_016708435.1_ASM1670843v1_genomic.fna.gz --refList GCA_016708435.1_ASM1670843v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708435.1_ASM1670843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:12:03,366] [INFO] Task succeeded: fastANI
[2023-06-30 14:12:03,377] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:12:03,377] [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
GCA_016708435.1	s__UBA2033 sp016708435	100.0	2023	2027	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__UBA2033	95.0	98.76	98.26	0.93	0.92	5	conclusive
GCA_002333425.1	s__UBA2033 sp002333425	79.7559	791	2027	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__UBA2033	95.0	99.51	99.51	0.83	0.83	2	-
GCA_017996175.1	s__UBA2033 sp017996175	79.6522	768	2027	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__UBA2033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711485.1	s__UBA2033 sp016711485	79.2939	748	2027	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__UBA2033	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332515.2	s__Leptospira_A wolbachii	76.4063	50	2027	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_015075105.1	s__JABWCC01 sp013359315	76.2627	60	2027	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__JABWCC01	95.0	99.74	99.74	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-30 14:12:03,380] [INFO] GTDB search result was written to GCA_016708435.1_ASM1670843v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:12:03,380] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:12:03,383] [INFO] DFAST_QC result json was written to GCA_016708435.1_ASM1670843v1_genomic.fna/dqc_result.json
[2023-06-30 14:12:03,383] [INFO] DFAST_QC completed!
[2023-06-30 14:12:03,383] [INFO] Total running time: 0h1m19s