[2024-01-24 14:05:33,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference
[2024-01-24 14:05:35,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,297] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,297] [INFO] Running command: gunzip -c /var/lib/cwl/stge5c31203-78ba-4e41-9a4d-f1180ea68308/GCF_004771005.1_ASM477100v1_genomic.fna.gz | prodigal -d GCF_004771005.1_ASM477100v1_genomic.fna/cds.fna -a GCF_004771005.1_ASM477100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:46,207] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:46,208] [INFO] Task started: HMMsearch
[2024-01-24 14:05:46,208] [INFO] Running command: hmmsearch --tblout GCF_004771005.1_ASM477100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference/reference_markers.hmm GCF_004771005.1_ASM477100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:46,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:46,535] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,576] [INFO] Query marker FASTA was written to GCF_004771005.1_ASM477100v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,577] [INFO] Task started: Blastn
[2024-01-24 14:05:46,577] [INFO] Running command: blastn -query GCF_004771005.1_ASM477100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference/reference_markers.fasta -out GCF_004771005.1_ASM477100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:47,145] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:47,148] [INFO] Selected 12 target genomes.
[2024-01-24 14:05:47,149] [INFO] Target genome list was writen to GCF_004771005.1_ASM477100v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:47,154] [INFO] Task started: fastANI
[2024-01-24 14:05:47,155] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c31203-78ba-4e41-9a4d-f1180ea68308/GCF_004771005.1_ASM477100v1_genomic.fna.gz --refList GCF_004771005.1_ASM477100v1_genomic.fna/target_genomes.txt --output GCF_004771005.1_ASM477100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:56,977] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:56,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:56,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:56,989] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:56,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:56,989] [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 ilyithenensis	strain=201400974	GCA_004771005.1	2484901	2484901	type	True	100.0	1369	1371	95	conclusive
Leptospira kobayashii	strain=E30	GCA_003114835.3	1917830	1917830	type	True	88.0391	1200	1371	95	below_threshold
Leptospira ognonensis	strain=201702476	GCA_004770745.1	2484945	2484945	type	True	77.3422	193	1371	95	below_threshold
Leptospira terpstrae	strain=LT 11-33	GCA_000332495.2	293075	293075	type	True	77.2344	246	1371	95	below_threshold
Leptospira levettii	strain=MCA2-B-A1	GCA_002812085.1	2023178	2023178	type	True	77.2308	209	1371	95	below_threshold
Leptospira meyeri	strain=DSM 21537	GCA_004368965.1	29508	29508	type	True	77.1136	228	1371	95	below_threshold
Leptospira chreensis	strain=201903075	GCA_016919165.1	2810035	2810035	type	True	77.0541	240	1371	95	below_threshold
Leptospira ellinghausenii	strain=E18	GCA_003114815.1	1917822	1917822	type	True	77.0523	211	1371	95	below_threshold
Leptospira brenneri	strain=JW2-C-A2	GCA_002812125.1	2023182	2023182	type	True	76.9234	243	1371	95	below_threshold
Leptospira ryugenii	strain=YH101	GCA_003114855.1	1917863	1917863	type	True	76.8338	138	1371	95	below_threshold
Leptospira ainazelensis	strain=201903071	GCA_016918785.1	2810034	2810034	type	True	75.948	58	1371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:56,991] [INFO] DFAST Taxonomy check result was written to GCF_004771005.1_ASM477100v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:56,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:56,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:56,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference/checkm_data
[2024-01-24 14:05:56,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:57,040] [INFO] Task started: CheckM
[2024-01-24 14:05:57,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004771005.1_ASM477100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004771005.1_ASM477100v1_genomic.fna/checkm_input GCF_004771005.1_ASM477100v1_genomic.fna/checkm_result
[2024-01-24 14:06:33,900] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:33,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:33,920] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:33,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:33,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004771005.1_ASM477100v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:33,922] [INFO] Task started: Blastn
[2024-01-24 14:06:33,922] [INFO] Running command: blastn -query GCF_004771005.1_ASM477100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfef10948-ba35-4fd5-8c0f-dab966c44575/dqc_reference/reference_markers_gtdb.fasta -out GCF_004771005.1_ASM477100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:34,773] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:34,776] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:34,777] [INFO] Target genome list was writen to GCF_004771005.1_ASM477100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:34,790] [INFO] Task started: fastANI
[2024-01-24 14:06:34,790] [INFO] Running command: fastANI --query /var/lib/cwl/stge5c31203-78ba-4e41-9a4d-f1180ea68308/GCF_004771005.1_ASM477100v1_genomic.fna.gz --refList GCF_004771005.1_ASM477100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004771005.1_ASM477100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:44,557] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:44,569] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:44,569] [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_004771005.1	s__Leptospira_A ilyithenensis	100.0	1369	1371	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003114835.1	s__Leptospira_A kobayashii	88.0421	1200	1371	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_004770995.1	s__Leptospira_A idonii	78.391	474	1371	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_004769575.1	s__Leptospira_A perdikensis	77.4222	219	1371	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_004770745.1	s__Leptospira_A ognonensis	77.3422	193	1371	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_004770265.1	s__Leptospira_A congkakensis	77.2679	227	1371	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.99	99.99	1.00	1.00	3	-
GCF_004770905.1	s__Leptospira_A bandrabouensis	77.2422	240	1371	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000332495.1	s__Leptospira_A terpstrae	77.2344	246	1371	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_002812085.1	s__Leptospira_A levettii	77.2325	208	1371	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	98.63	98.25	0.94	0.91	14	-
GCF_003114815.1	s__Leptospira_A ellinghausenii	77.0523	211	1371	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_004770145.1	s__Leptospira_A bourretii	77.0098	268	1371	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.12	99.11	0.96	0.96	4	-
GCF_002812125.1	s__Leptospira_A brenneri	76.9139	244	1371	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A	95.0	99.47	99.47	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,571] [INFO] GTDB search result was written to GCF_004771005.1_ASM477100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:44,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:44,577] [INFO] DFAST_QC result json was written to GCF_004771005.1_ASM477100v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:44,577] [INFO] DFAST_QC completed!
[2024-01-24 14:06:44,577] [INFO] Total running time: 0h1m11s