[2024-01-24 14:12:35,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:35,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:35,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference
[2024-01-24 14:12:37,052] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:37,053] [INFO] Task started: Prodigal
[2024-01-24 14:12:37,054] [INFO] Running command: gunzip -c /var/lib/cwl/stg779640b3-f4f3-457a-9a30-618e04ed529b/GCF_000154825.1_ASM15482v1_genomic.fna.gz | prodigal -d GCF_000154825.1_ASM15482v1_genomic.fna/cds.fna -a GCF_000154825.1_ASM15482v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:41,650] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:41,650] [INFO] Task started: HMMsearch
[2024-01-24 14:12:41,650] [INFO] Running command: hmmsearch --tblout GCF_000154825.1_ASM15482v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference/reference_markers.hmm GCF_000154825.1_ASM15482v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:41,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:41,877] [INFO] Found 6/6 markers.
[2024-01-24 14:12:41,903] [INFO] Query marker FASTA was written to GCF_000154825.1_ASM15482v1_genomic.fna/markers.fasta
[2024-01-24 14:12:41,903] [INFO] Task started: Blastn
[2024-01-24 14:12:41,903] [INFO] Running command: blastn -query GCF_000154825.1_ASM15482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference/reference_markers.fasta -out GCF_000154825.1_ASM15482v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:42,520] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:42,525] [INFO] Selected 14 target genomes.
[2024-01-24 14:12:42,527] [INFO] Target genome list was writen to GCF_000154825.1_ASM15482v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:42,560] [INFO] Task started: fastANI
[2024-01-24 14:12:42,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg779640b3-f4f3-457a-9a30-618e04ed529b/GCF_000154825.1_ASM15482v1_genomic.fna.gz --refList GCF_000154825.1_ASM15482v1_genomic.fna/target_genomes.txt --output GCF_000154825.1_ASM15482v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:49,565] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:49,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:49,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:49,569] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:49,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:49,569] [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
Anaerofustis stercorihominis	strain=DSM 17244	GCA_000154825.1	214853	214853	type	True	100.0	759	759	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:12:49,570] [INFO] DFAST Taxonomy check result was written to GCF_000154825.1_ASM15482v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:49,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:49,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:49,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference/checkm_data
[2024-01-24 14:12:49,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:49,599] [INFO] Task started: CheckM
[2024-01-24 14:12:49,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000154825.1_ASM15482v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000154825.1_ASM15482v1_genomic.fna/checkm_input GCF_000154825.1_ASM15482v1_genomic.fna/checkm_result
[2024-01-24 14:13:10,244] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:10,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:10,263] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:10,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:10,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000154825.1_ASM15482v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:10,265] [INFO] Task started: Blastn
[2024-01-24 14:13:10,265] [INFO] Running command: blastn -query GCF_000154825.1_ASM15482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47cb5474-ab08-41f2-8bb8-5063491920f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000154825.1_ASM15482v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:11,088] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:11,092] [INFO] Selected 14 target genomes.
[2024-01-24 14:13:11,092] [INFO] Target genome list was writen to GCF_000154825.1_ASM15482v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:11,102] [INFO] Task started: fastANI
[2024-01-24 14:13:11,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg779640b3-f4f3-457a-9a30-618e04ed529b/GCF_000154825.1_ASM15482v1_genomic.fna.gz --refList GCF_000154825.1_ASM15482v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000154825.1_ASM15482v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:20,070] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:20,078] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:20,078] [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_000154825.1	s__Anaerofustis stercorihominis	100.0	758	759	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Anaerofustaceae;g__Anaerofustis	95.0	99.00	97.99	0.96	0.91	3	conclusive
GCA_900549875.1	s__Anaerofustis sp900549875	89.2566	614	759	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Anaerofustaceae;g__Anaerofustis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005844425.1	s__Anaerofustis stercorihominis_A	79.5365	265	759	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Anaerofustaceae;g__Anaerofustis	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:20,080] [INFO] GTDB search result was written to GCF_000154825.1_ASM15482v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:20,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:20,084] [INFO] DFAST_QC result json was written to GCF_000154825.1_ASM15482v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:20,084] [INFO] DFAST_QC completed!
[2024-01-24 14:13:20,085] [INFO] Total running time: 0h0m44s