[2023-06-05 10:36:38,359] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:36:38,362] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:36:38,362] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference
[2023-06-05 10:36:41,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:36:41,028] [INFO] Task started: Prodigal
[2023-06-05 10:36:41,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg87ccb6a6-97a6-4656-b9b4-ddf4cb4f3071/GCA_001899385.1_ASM189938v1_genomic.fna.gz | prodigal -d GCA_001899385.1_ASM189938v1_genomic.fna/cds.fna -a GCA_001899385.1_ASM189938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:36:43,511] [INFO] Task succeeded: Prodigal
[2023-06-05 10:36:43,512] [INFO] Task started: HMMsearch
[2023-06-05 10:36:43,512] [INFO] Running command: hmmsearch --tblout GCA_001899385.1_ASM189938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference/reference_markers.hmm GCA_001899385.1_ASM189938v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:36:43,740] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:36:43,741] [INFO] Found 6/6 markers.
[2023-06-05 10:36:43,762] [INFO] Query marker FASTA was written to GCA_001899385.1_ASM189938v1_genomic.fna/markers.fasta
[2023-06-05 10:36:43,762] [INFO] Task started: Blastn
[2023-06-05 10:36:43,762] [INFO] Running command: blastn -query GCA_001899385.1_ASM189938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference/reference_markers.fasta -out GCA_001899385.1_ASM189938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:36:45,453] [INFO] Task succeeded: Blastn
[2023-06-05 10:36:45,458] [INFO] Selected 17 target genomes.
[2023-06-05 10:36:45,458] [INFO] Target genome list was writen to GCA_001899385.1_ASM189938v1_genomic.fna/target_genomes.txt
[2023-06-05 10:36:45,465] [INFO] Task started: fastANI
[2023-06-05 10:36:45,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ccb6a6-97a6-4656-b9b4-ddf4cb4f3071/GCA_001899385.1_ASM189938v1_genomic.fna.gz --refList GCA_001899385.1_ASM189938v1_genomic.fna/target_genomes.txt --output GCA_001899385.1_ASM189938v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:36:53,110] [INFO] Task succeeded: fastANI
[2023-06-05 10:36:53,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:36:53,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:36:53,118] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:36:53,118] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:36:53,118] [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
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	75.3185	56	581	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	75.1633	54	581	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	75.0169	54	581	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	74.8549	77	581	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:36:53,121] [INFO] DFAST Taxonomy check result was written to GCA_001899385.1_ASM189938v1_genomic.fna/tc_result.tsv
[2023-06-05 10:36:53,121] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:36:53,122] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:36:53,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference/checkm_data
[2023-06-05 10:36:53,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:36:53,152] [INFO] Task started: CheckM
[2023-06-05 10:36:53,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001899385.1_ASM189938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001899385.1_ASM189938v1_genomic.fna/checkm_input GCA_001899385.1_ASM189938v1_genomic.fna/checkm_result
[2023-06-05 10:37:10,136] [INFO] Task succeeded: CheckM
[2023-06-05 10:37:10,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:37:10,173] [INFO] ===== Completeness check finished =====
[2023-06-05 10:37:10,173] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:37:10,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001899385.1_ASM189938v1_genomic.fna/markers.fasta)
[2023-06-05 10:37:10,174] [INFO] Task started: Blastn
[2023-06-05 10:37:10,174] [INFO] Running command: blastn -query GCA_001899385.1_ASM189938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb73effa-a61f-4c74-b3c0-c3ced2455755/dqc_reference/reference_markers_gtdb.fasta -out GCA_001899385.1_ASM189938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:37:10,961] [INFO] Task succeeded: Blastn
[2023-06-05 10:37:10,968] [INFO] Selected 17 target genomes.
[2023-06-05 10:37:10,968] [INFO] Target genome list was writen to GCA_001899385.1_ASM189938v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:37:11,098] [INFO] Task started: fastANI
[2023-06-05 10:37:11,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ccb6a6-97a6-4656-b9b4-ddf4cb4f3071/GCA_001899385.1_ASM189938v1_genomic.fna.gz --refList GCA_001899385.1_ASM189938v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001899385.1_ASM189938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:37:16,656] [INFO] Task succeeded: fastANI
[2023-06-05 10:37:16,666] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:37:16,666] [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_001899385.1	s__Caenarcanum bioreactoricola	99.9977	554	581	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Caenarcaniphilales;f__Caenarcanaceae;g__Caenarcanum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016744535.1	s__BB28 sp016744535	74.8989	71	581	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__BB28;g__BB28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215945.1	s__NORP36 sp004566295	74.7323	56	581	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	99.94	99.94	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-05 10:37:16,669] [INFO] GTDB search result was written to GCA_001899385.1_ASM189938v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:37:16,669] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:37:16,672] [INFO] DFAST_QC result json was written to GCA_001899385.1_ASM189938v1_genomic.fna/dqc_result.json
[2023-06-05 10:37:16,673] [INFO] DFAST_QC completed!
[2023-06-05 10:37:16,673] [INFO] Total running time: 0h0m38s