[2024-01-24 12:44:11,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,209] [INFO] DQC Reference Directory: /var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference
[2024-01-24 12:44:12,549] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,550] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,550] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb29f0ea-9617-417e-83e1-a15accbc049c/GCF_004362975.1_ASM436297v1_genomic.fna.gz | prodigal -d GCF_004362975.1_ASM436297v1_genomic.fna/cds.fna -a GCF_004362975.1_ASM436297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:17,758] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:17,759] [INFO] Task started: HMMsearch
[2024-01-24 12:44:17,759] [INFO] Running command: hmmsearch --tblout GCF_004362975.1_ASM436297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference/reference_markers.hmm GCF_004362975.1_ASM436297v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:18,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:18,047] [INFO] Found 6/6 markers.
[2024-01-24 12:44:18,080] [INFO] Query marker FASTA was written to GCF_004362975.1_ASM436297v1_genomic.fna/markers.fasta
[2024-01-24 12:44:18,081] [INFO] Task started: Blastn
[2024-01-24 12:44:18,081] [INFO] Running command: blastn -query GCF_004362975.1_ASM436297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference/reference_markers.fasta -out GCF_004362975.1_ASM436297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:18,680] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:18,683] [INFO] Selected 19 target genomes.
[2024-01-24 12:44:18,684] [INFO] Target genome list was writen to GCF_004362975.1_ASM436297v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:18,713] [INFO] Task started: fastANI
[2024-01-24 12:44:18,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb29f0ea-9617-417e-83e1-a15accbc049c/GCF_004362975.1_ASM436297v1_genomic.fna.gz --refList GCF_004362975.1_ASM436297v1_genomic.fna/target_genomes.txt --output GCF_004362975.1_ASM436297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:29,571] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:29,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:29,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:29,578] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:29,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:29,578] [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
Aminicella lysinilytica	strain=DSM 28287	GCA_004362975.1	433323	433323	type	True	100.0	715	718	95	conclusive
Emergencia timonensis	strain=SN18	GCA_900086585.1	1776384	1776384	type	True	77.5443	58	718	95	below_threshold
Hornefia butyriciproducens	strain=WCA-MUC-591-APC-3H	GCA_009695915.1	2652293	2652293	type	True	77.4769	71	718	95	below_threshold
Hornefia porci	strain=68-3-10	GCA_001940235.1	2652292	2652292	type	True	77.2859	81	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:29,580] [INFO] DFAST Taxonomy check result was written to GCF_004362975.1_ASM436297v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:29,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:29,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:29,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference/checkm_data
[2024-01-24 12:44:29,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:29,614] [INFO] Task started: CheckM
[2024-01-24 12:44:29,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362975.1_ASM436297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362975.1_ASM436297v1_genomic.fna/checkm_input GCF_004362975.1_ASM436297v1_genomic.fna/checkm_result
[2024-01-24 12:44:53,325] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:53,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:53,353] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:53,353] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:53,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362975.1_ASM436297v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:53,354] [INFO] Task started: Blastn
[2024-01-24 12:44:53,354] [INFO] Running command: blastn -query GCF_004362975.1_ASM436297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga539a4b0-fb77-47fe-b522-1e6533a55438/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362975.1_ASM436297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:54,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:54,244] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:54,245] [INFO] Target genome list was writen to GCF_004362975.1_ASM436297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:54,274] [INFO] Task started: fastANI
[2024-01-24 12:44:54,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb29f0ea-9617-417e-83e1-a15accbc049c/GCF_004362975.1_ASM436297v1_genomic.fna.gz --refList GCF_004362975.1_ASM436297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362975.1_ASM436297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:00,691] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:00,697] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:00,697] [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_004362975.1	s__Aminicella lysinilytica	100.0	715	718	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminicella	95.0	96.40	96.40	0.90	0.90	2	conclusive
GCF_009695915.1	s__Hornefia butyriciproducens	77.5173	70	718	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Hornefia	95.0	98.31	98.09	0.84	0.77	13	-
GCA_902362805.1	s__Emergencia sp900066695	77.3801	60	718	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Emergencia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001940235.1	s__Hornefia porci	77.3024	82	718	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Hornefia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315125.1	s__Hornefia sp900315125	76.5732	77	718	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Hornefia	95.0	99.94	99.94	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:00,699] [INFO] GTDB search result was written to GCF_004362975.1_ASM436297v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:00,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:00,702] [INFO] DFAST_QC result json was written to GCF_004362975.1_ASM436297v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:00,703] [INFO] DFAST_QC completed!
[2024-01-24 12:45:00,703] [INFO] Total running time: 0h0m49s