[2024-01-24 10:57:26,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,825] [INFO] DQC Reference Directory: /var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference
[2024-01-24 10:57:28,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,180] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,181] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf88d9b9-4918-4c8f-9943-60e397605f59/GCF_020097375.1_ASM2009737v1_genomic.fna.gz | prodigal -d GCF_020097375.1_ASM2009737v1_genomic.fna/cds.fna -a GCF_020097375.1_ASM2009737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:38,526] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:38,526] [INFO] Task started: HMMsearch
[2024-01-24 10:57:38,526] [INFO] Running command: hmmsearch --tblout GCF_020097375.1_ASM2009737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference/reference_markers.hmm GCF_020097375.1_ASM2009737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:38,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:38,746] [INFO] Found 6/6 markers.
[2024-01-24 10:57:38,777] [INFO] Query marker FASTA was written to GCF_020097375.1_ASM2009737v1_genomic.fna/markers.fasta
[2024-01-24 10:57:38,778] [INFO] Task started: Blastn
[2024-01-24 10:57:38,778] [INFO] Running command: blastn -query GCF_020097375.1_ASM2009737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference/reference_markers.fasta -out GCF_020097375.1_ASM2009737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:39,389] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:39,392] [INFO] Selected 12 target genomes.
[2024-01-24 10:57:39,392] [INFO] Target genome list was writen to GCF_020097375.1_ASM2009737v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:39,415] [INFO] Task started: fastANI
[2024-01-24 10:57:39,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf88d9b9-4918-4c8f-9943-60e397605f59/GCF_020097375.1_ASM2009737v1_genomic.fna.gz --refList GCF_020097375.1_ASM2009737v1_genomic.fna/target_genomes.txt --output GCF_020097375.1_ASM2009737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:44,610] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:44,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:44,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:44,618] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:57:44,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:44,618] [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 endodontalis	strain=FDAARGOS_1506	GCA_020097375.1	28124	28124	type	True	100.0	699	700	95	conclusive
Porphyromonas endodontalis	strain=NCTC13058	GCA_900454815.1	28124	28124	type	True	99.9987	698	700	95	conclusive
Porphyromonas endodontalis	strain=ATCC 35406	GCA_000174815.1	28124	28124	type	True	99.9647	664	700	95	conclusive
Porphyromonas gingivicanis	strain=JCM 15907	GCA_000614585.1	266762	266762	type	True	77.465	70	700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:44,620] [INFO] DFAST Taxonomy check result was written to GCF_020097375.1_ASM2009737v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:44,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:44,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:44,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference/checkm_data
[2024-01-24 10:57:44,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:44,646] [INFO] Task started: CheckM
[2024-01-24 10:57:44,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097375.1_ASM2009737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097375.1_ASM2009737v1_genomic.fna/checkm_input GCF_020097375.1_ASM2009737v1_genomic.fna/checkm_result
[2024-01-24 10:58:18,152] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:18,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:18,170] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:18,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:18,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097375.1_ASM2009737v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:18,171] [INFO] Task started: Blastn
[2024-01-24 10:58:18,171] [INFO] Running command: blastn -query GCF_020097375.1_ASM2009737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0229ea8-c8da-45cd-818a-abeccf343260/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097375.1_ASM2009737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:19,016] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:19,020] [INFO] Selected 28 target genomes.
[2024-01-24 10:58:19,020] [INFO] Target genome list was writen to GCF_020097375.1_ASM2009737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:19,079] [INFO] Task started: fastANI
[2024-01-24 10:58:19,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf88d9b9-4918-4c8f-9943-60e397605f59/GCF_020097375.1_ASM2009737v1_genomic.fna.gz --refList GCF_020097375.1_ASM2009737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097375.1_ASM2009737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:31,112] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,116] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:31,116] [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_000174815.1	s__Porphyromonas endodontalis	99.9647	664	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.24	96.48	0.96	0.91	3	conclusive
GCF_000614585.1	s__Porphyromonas gingivicanis	77.4599	71	700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas	95.0	98.86	98.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,117] [INFO] GTDB search result was written to GCF_020097375.1_ASM2009737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:31,118] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:31,120] [INFO] DFAST_QC result json was written to GCF_020097375.1_ASM2009737v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:31,120] [INFO] DFAST_QC completed!
[2024-01-24 10:58:31,120] [INFO] Total running time: 0h1m4s