[2024-01-24 12:48:05,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:05,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:05,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference
[2024-01-24 12:48:06,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:06,259] [INFO] Task started: Prodigal
[2024-01-24 12:48:06,259] [INFO] Running command: gunzip -c /var/lib/cwl/stg245e2b33-eace-47a8-98a2-cd3550d35392/GCF_004341825.1_ASM434182v1_genomic.fna.gz | prodigal -d GCF_004341825.1_ASM434182v1_genomic.fna/cds.fna -a GCF_004341825.1_ASM434182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:13,221] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:13,222] [INFO] Task started: HMMsearch
[2024-01-24 12:48:13,222] [INFO] Running command: hmmsearch --tblout GCF_004341825.1_ASM434182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference/reference_markers.hmm GCF_004341825.1_ASM434182v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:13,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:13,522] [INFO] Found 6/6 markers.
[2024-01-24 12:48:13,552] [INFO] Query marker FASTA was written to GCF_004341825.1_ASM434182v1_genomic.fna/markers.fasta
[2024-01-24 12:48:13,552] [INFO] Task started: Blastn
[2024-01-24 12:48:13,552] [INFO] Running command: blastn -query GCF_004341825.1_ASM434182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference/reference_markers.fasta -out GCF_004341825.1_ASM434182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:14,150] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:14,154] [INFO] Selected 21 target genomes.
[2024-01-24 12:48:14,155] [INFO] Target genome list was writen to GCF_004341825.1_ASM434182v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:14,164] [INFO] Task started: fastANI
[2024-01-24 12:48:14,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg245e2b33-eace-47a8-98a2-cd3550d35392/GCF_004341825.1_ASM434182v1_genomic.fna.gz --refList GCF_004341825.1_ASM434182v1_genomic.fna/target_genomes.txt --output GCF_004341825.1_ASM434182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:24,905] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:24,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:24,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:24,910] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:24,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:24,910] [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
Hazenella coriacea	strain=DSM 45707	GCA_004341825.1	1179467	1179467	type	True	100.0	1001	1001	95	conclusive
Thermoflavimicrobium dichotomicum	strain=DSM 44778	GCA_900114055.1	46223	46223	type	True	76.6583	67	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:24,916] [INFO] DFAST Taxonomy check result was written to GCF_004341825.1_ASM434182v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:24,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:24,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:24,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference/checkm_data
[2024-01-24 12:48:24,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:24,952] [INFO] Task started: CheckM
[2024-01-24 12:48:24,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341825.1_ASM434182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341825.1_ASM434182v1_genomic.fna/checkm_input GCF_004341825.1_ASM434182v1_genomic.fna/checkm_result
[2024-01-24 12:48:54,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:54,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:54,707] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:54,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:54,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341825.1_ASM434182v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:54,709] [INFO] Task started: Blastn
[2024-01-24 12:48:54,709] [INFO] Running command: blastn -query GCF_004341825.1_ASM434182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg259df59a-5343-4a04-8c7a-740c7d3d4b6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341825.1_ASM434182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:55,583] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:55,588] [INFO] Selected 21 target genomes.
[2024-01-24 12:48:55,589] [INFO] Target genome list was writen to GCF_004341825.1_ASM434182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:55,604] [INFO] Task started: fastANI
[2024-01-24 12:48:55,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg245e2b33-eace-47a8-98a2-cd3550d35392/GCF_004341825.1_ASM434182v1_genomic.fna.gz --refList GCF_004341825.1_ASM434182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341825.1_ASM434182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:07,321] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:07,327] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:07,327] [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_004341825.1	s__Hazenella coriacea	100.0	1001	1001	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Hazenella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114055.1	s__Thermoflavimicrobium dichotomicum	76.6924	66	1001	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoflavimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:07,332] [INFO] GTDB search result was written to GCF_004341825.1_ASM434182v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:07,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:07,335] [INFO] DFAST_QC result json was written to GCF_004341825.1_ASM434182v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:07,336] [INFO] DFAST_QC completed!
[2024-01-24 12:49:07,336] [INFO] Total running time: 0h1m2s