[2024-01-24 14:06:06,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference
[2024-01-24 14:06:08,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,354] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d97c4ec-714a-4798-84c1-aba0e401dfe1/GCF_001306175.1_ASM130617v1_genomic.fna.gz | prodigal -d GCF_001306175.1_ASM130617v1_genomic.fna/cds.fna -a GCF_001306175.1_ASM130617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:22,939] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:22,940] [INFO] Task started: HMMsearch
[2024-01-24 14:06:22,940] [INFO] Running command: hmmsearch --tblout GCF_001306175.1_ASM130617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference/reference_markers.hmm GCF_001306175.1_ASM130617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:23,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:23,290] [INFO] Found 6/6 markers.
[2024-01-24 14:06:23,331] [INFO] Query marker FASTA was written to GCF_001306175.1_ASM130617v1_genomic.fna/markers.fasta
[2024-01-24 14:06:23,332] [INFO] Task started: Blastn
[2024-01-24 14:06:23,332] [INFO] Running command: blastn -query GCF_001306175.1_ASM130617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference/reference_markers.fasta -out GCF_001306175.1_ASM130617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:24,069] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:24,072] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:24,073] [INFO] Target genome list was writen to GCF_001306175.1_ASM130617v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:24,088] [INFO] Task started: fastANI
[2024-01-24 14:06:24,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d97c4ec-714a-4798-84c1-aba0e401dfe1/GCF_001306175.1_ASM130617v1_genomic.fna.gz --refList GCF_001306175.1_ASM130617v1_genomic.fna/target_genomes.txt --output GCF_001306175.1_ASM130617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:36,625] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:36,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:36,630] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:36,630] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:36,630] [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
Ardenticatena maritima	strain=110S	GCA_001306175.1	872965	872965	type	True	100.0	1181	1182	95	conclusive
Ardenticatena maritima	strain=110S	GCA_001293545.1	872965	872965	type	True	99.8328	1047	1182	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,632] [INFO] DFAST Taxonomy check result was written to GCF_001306175.1_ASM130617v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:36,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:36,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:36,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference/checkm_data
[2024-01-24 14:06:36,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:36,681] [INFO] Task started: CheckM
[2024-01-24 14:06:36,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001306175.1_ASM130617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001306175.1_ASM130617v1_genomic.fna/checkm_input GCF_001306175.1_ASM130617v1_genomic.fna/checkm_result
[2024-01-24 14:07:26,960] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:26,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,987] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:26,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:26,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001306175.1_ASM130617v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:26,988] [INFO] Task started: Blastn
[2024-01-24 14:07:26,988] [INFO] Running command: blastn -query GCF_001306175.1_ASM130617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a7a9666-f53d-419b-aeb6-587943de3953/dqc_reference/reference_markers_gtdb.fasta -out GCF_001306175.1_ASM130617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:27,816] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:27,820] [INFO] Selected 16 target genomes.
[2024-01-24 14:07:27,820] [INFO] Target genome list was writen to GCF_001306175.1_ASM130617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:27,861] [INFO] Task started: fastANI
[2024-01-24 14:07:27,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d97c4ec-714a-4798-84c1-aba0e401dfe1/GCF_001306175.1_ASM130617v1_genomic.fna.gz --refList GCF_001306175.1_ASM130617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001306175.1_ASM130617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:37,477] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:37,482] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:37,482] [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_001306175.1	s__Ardenticatena maritima	100.0	1181	1182	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__Ardenticatena	95.0	98.28	96.57	0.97	0.94	3	conclusive
GCA_015487975.1	s__Ardenticatena sp015487975	80.4199	706	1182	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__Ardenticatena	95.0	99.35	99.35	0.98	0.98	2	-
GCA_015491235.1	s__WFWG01 sp015491235	76.5104	144	1182	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__WFWG01	95.0	99.02	98.95	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:37,483] [INFO] GTDB search result was written to GCF_001306175.1_ASM130617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:37,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:37,486] [INFO] DFAST_QC result json was written to GCF_001306175.1_ASM130617v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:37,486] [INFO] DFAST_QC completed!
[2024-01-24 14:07:37,486] [INFO] Total running time: 0h1m31s