[2024-01-24 13:27:42,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:42,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:42,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference
[2024-01-24 13:27:43,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:43,304] [INFO] Task started: Prodigal
[2024-01-24 13:27:43,304] [INFO] Running command: gunzip -c /var/lib/cwl/stgf56b4dd9-d12e-4306-80cd-c346983358e7/GCF_000378065.1_ASM37806v1_genomic.fna.gz | prodigal -d GCF_000378065.1_ASM37806v1_genomic.fna/cds.fna -a GCF_000378065.1_ASM37806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:55,936] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:55,937] [INFO] Task started: HMMsearch
[2024-01-24 13:27:55,937] [INFO] Running command: hmmsearch --tblout GCF_000378065.1_ASM37806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference/reference_markers.hmm GCF_000378065.1_ASM37806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:56,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:56,214] [INFO] Found 6/6 markers.
[2024-01-24 13:27:56,241] [INFO] Query marker FASTA was written to GCF_000378065.1_ASM37806v1_genomic.fna/markers.fasta
[2024-01-24 13:27:56,241] [INFO] Task started: Blastn
[2024-01-24 13:27:56,241] [INFO] Running command: blastn -query GCF_000378065.1_ASM37806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference/reference_markers.fasta -out GCF_000378065.1_ASM37806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:56,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:56,842] [INFO] Selected 12 target genomes.
[2024-01-24 13:27:56,842] [INFO] Target genome list was writen to GCF_000378065.1_ASM37806v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:56,850] [INFO] Task started: fastANI
[2024-01-24 13:27:56,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgf56b4dd9-d12e-4306-80cd-c346983358e7/GCF_000378065.1_ASM37806v1_genomic.fna.gz --refList GCF_000378065.1_ASM37806v1_genomic.fna/target_genomes.txt --output GCF_000378065.1_ASM37806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:04,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:04,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:04,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:04,870] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:04,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:04,870] [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
Porphyromonas gulae	strain=DSM 15663	GCA_000378065.1	111105	111105	type	True	100.0	735	738	95	conclusive
Porphyromonas gingivalis	strain=ATCC 33277	GCA_002892575.1	837	837	type	True	92.2303	612	738	95	below_threshold
Porphyromonas gingivalis	strain=ATCC 33277	GCA_000010505.1	837	837	type	True	92.1899	619	738	95	below_threshold
Porphyromonas loveana	strain=DSM 28520	GCA_003096695.1	1884669	1884669	type	True	79.2219	298	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:04,872] [INFO] DFAST Taxonomy check result was written to GCF_000378065.1_ASM37806v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:04,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:04,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:04,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference/checkm_data
[2024-01-24 13:28:04,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:04,907] [INFO] Task started: CheckM
[2024-01-24 13:28:04,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378065.1_ASM37806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378065.1_ASM37806v1_genomic.fna/checkm_input GCF_000378065.1_ASM37806v1_genomic.fna/checkm_result
[2024-01-24 13:28:45,300] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:45,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:45,325] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:45,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:45,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378065.1_ASM37806v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:45,326] [INFO] Task started: Blastn
[2024-01-24 13:28:45,326] [INFO] Running command: blastn -query GCF_000378065.1_ASM37806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b737a6b-5884-4286-9df3-f5b952cb48ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378065.1_ASM37806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:46,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:46,173] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:46,173] [INFO] Target genome list was writen to GCF_000378065.1_ASM37806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:46,257] [INFO] Task started: fastANI
[2024-01-24 13:28:46,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgf56b4dd9-d12e-4306-80cd-c346983358e7/GCF_000378065.1_ASM37806v1_genomic.fna.gz --refList GCF_000378065.1_ASM37806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378065.1_ASM37806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:56,827] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:56,834] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:56,834] [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_000378065.1	s__Porphyromonas gulae	100.0	735	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.30	97.40	0.91	0.87	13	conclusive
GCF_000010505.1	s__Porphyromonas gingivalis	92.1587	621	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.32	97.95	0.91	0.84	70	-
GCF_003096695.1	s__Porphyromonas loveana	79.2218	298	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,836] [INFO] GTDB search result was written to GCF_000378065.1_ASM37806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:56,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:56,840] [INFO] DFAST_QC result json was written to GCF_000378065.1_ASM37806v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:56,840] [INFO] DFAST_QC completed!
[2024-01-24 13:28:56,840] [INFO] Total running time: 0h1m15s