[2024-01-24 11:34:39,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:39,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:39,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference
[2024-01-24 11:34:40,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:40,824] [INFO] Task started: Prodigal
[2024-01-24 11:34:40,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg14baa946-17a6-431b-8291-c303bd1c8460/GCF_002892575.1_ASM289257v1_genomic.fna.gz | prodigal -d GCF_002892575.1_ASM289257v1_genomic.fna/cds.fna -a GCF_002892575.1_ASM289257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,856] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,857] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,857] [INFO] Running command: hmmsearch --tblout GCF_002892575.1_ASM289257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference/reference_markers.hmm GCF_002892575.1_ASM289257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,107] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,128] [INFO] Query marker FASTA was written to GCF_002892575.1_ASM289257v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,128] [INFO] Task started: Blastn
[2024-01-24 11:34:54,128] [INFO] Running command: blastn -query GCF_002892575.1_ASM289257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference/reference_markers.fasta -out GCF_002892575.1_ASM289257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,743] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,747] [INFO] Selected 13 target genomes.
[2024-01-24 11:34:54,747] [INFO] Target genome list was writen to GCF_002892575.1_ASM289257v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,752] [INFO] Task started: fastANI
[2024-01-24 11:34:54,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg14baa946-17a6-431b-8291-c303bd1c8460/GCF_002892575.1_ASM289257v1_genomic.fna.gz --refList GCF_002892575.1_ASM289257v1_genomic.fna/target_genomes.txt --output GCF_002892575.1_ASM289257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:04,840] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:04,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:04,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:04,846] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:04,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:04,847] [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 gingivalis	strain=ATCC 33277	GCA_002892575.1	837	837	type	True	100.0	783	793	95	conclusive
Porphyromonas gingivalis	strain=ATCC 33277	GCA_000010505.1	837	837	type	True	99.9923	778	793	95	conclusive
Porphyromonas gulae	strain=DSM 15663	GCA_000378065.1	111105	111105	type	True	92.3279	606	793	95	below_threshold
Porphyromonas loveana	strain=DSM 28520	GCA_003096695.1	1884669	1884669	type	True	79.1554	297	793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:04,849] [INFO] DFAST Taxonomy check result was written to GCF_002892575.1_ASM289257v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:04,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:04,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:04,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference/checkm_data
[2024-01-24 11:35:04,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:04,877] [INFO] Task started: CheckM
[2024-01-24 11:35:04,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002892575.1_ASM289257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002892575.1_ASM289257v1_genomic.fna/checkm_input GCF_002892575.1_ASM289257v1_genomic.fna/checkm_result
[2024-01-24 11:35:45,050] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:45,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,067] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:45,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:45,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002892575.1_ASM289257v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:45,068] [INFO] Task started: Blastn
[2024-01-24 11:35:45,068] [INFO] Running command: blastn -query GCF_002892575.1_ASM289257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd522269c-40df-464f-98c4-6857e8e64784/dqc_reference/reference_markers_gtdb.fasta -out GCF_002892575.1_ASM289257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:45,887] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:45,891] [INFO] Selected 21 target genomes.
[2024-01-24 11:35:45,891] [INFO] Target genome list was writen to GCF_002892575.1_ASM289257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:45,915] [INFO] Task started: fastANI
[2024-01-24 11:35:45,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg14baa946-17a6-431b-8291-c303bd1c8460/GCF_002892575.1_ASM289257v1_genomic.fna.gz --refList GCF_002892575.1_ASM289257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002892575.1_ASM289257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:58,270] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:58,274] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:58,274] [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_000010505.1	s__Porphyromonas gingivalis	99.9922	775	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.32	97.95	0.91	0.84	70	conclusive
GCF_000378065.1	s__Porphyromonas gulae	92.3069	607	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.30	97.40	0.91	0.87	13	-
GCF_003096695.1	s__Porphyromonas loveana	79.1224	297	793	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 11:35:58,276] [INFO] GTDB search result was written to GCF_002892575.1_ASM289257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:58,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:58,279] [INFO] DFAST_QC result json was written to GCF_002892575.1_ASM289257v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:58,279] [INFO] DFAST_QC completed!
[2024-01-24 11:35:58,279] [INFO] Total running time: 0h1m19s