[2023-06-13 00:23:24,063] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:23:24,075] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:23:24,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference
[2023-06-13 00:23:25,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:23:25,310] [INFO] Task started: Prodigal
[2023-06-13 00:23:25,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a646236-2756-43f4-ad4d-8835277004c5/GCA_022720115.1_ASM2272011v1_genomic.fna.gz | prodigal -d GCA_022720115.1_ASM2272011v1_genomic.fna/cds.fna -a GCA_022720115.1_ASM2272011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:23:42,243] [INFO] Task succeeded: Prodigal
[2023-06-13 00:23:42,243] [INFO] Task started: HMMsearch
[2023-06-13 00:23:42,243] [INFO] Running command: hmmsearch --tblout GCA_022720115.1_ASM2272011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference/reference_markers.hmm GCA_022720115.1_ASM2272011v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:23:42,530] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:23:42,532] [INFO] Found 6/6 markers.
[2023-06-13 00:23:42,592] [INFO] Query marker FASTA was written to GCA_022720115.1_ASM2272011v1_genomic.fna/markers.fasta
[2023-06-13 00:23:42,592] [INFO] Task started: Blastn
[2023-06-13 00:23:42,593] [INFO] Running command: blastn -query GCA_022720115.1_ASM2272011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference/reference_markers.fasta -out GCA_022720115.1_ASM2272011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:23:43,209] [INFO] Task succeeded: Blastn
[2023-06-13 00:23:43,213] [INFO] Selected 12 target genomes.
[2023-06-13 00:23:43,214] [INFO] Target genome list was writen to GCA_022720115.1_ASM2272011v1_genomic.fna/target_genomes.txt
[2023-06-13 00:23:43,217] [INFO] Task started: fastANI
[2023-06-13 00:23:43,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a646236-2756-43f4-ad4d-8835277004c5/GCA_022720115.1_ASM2272011v1_genomic.fna.gz --refList GCA_022720115.1_ASM2272011v1_genomic.fna/target_genomes.txt --output GCA_022720115.1_ASM2272011v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:23:54,194] [INFO] Task succeeded: fastANI
[2023-06-13 00:23:54,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:23:54,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:23:54,207] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 00:23:54,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 00:23:54,208] [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
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	97.358	578	616	95	conclusive
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	97.3085	577	616	95	conclusive
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	97.3022	578	616	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	78.7005	149	616	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.6873	152	616	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	77.889	137	616	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	77.6487	142	616	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	77.6198	143	616	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.5685	141	616	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.5464	142	616	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:23:54,211] [INFO] DFAST Taxonomy check result was written to GCA_022720115.1_ASM2272011v1_genomic.fna/tc_result.tsv
[2023-06-13 00:23:54,213] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:23:54,214] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:23:54,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference/checkm_data
[2023-06-13 00:23:54,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:23:54,260] [INFO] Task started: CheckM
[2023-06-13 00:23:54,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022720115.1_ASM2272011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022720115.1_ASM2272011v1_genomic.fna/checkm_input GCA_022720115.1_ASM2272011v1_genomic.fna/checkm_result
[2023-06-13 00:24:42,733] [INFO] Task succeeded: CheckM
[2023-06-13 00:24:42,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:24:42,761] [INFO] ===== Completeness check finished =====
[2023-06-13 00:24:42,761] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:24:42,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022720115.1_ASM2272011v1_genomic.fna/markers.fasta)
[2023-06-13 00:24:42,762] [INFO] Task started: Blastn
[2023-06-13 00:24:42,762] [INFO] Running command: blastn -query GCA_022720115.1_ASM2272011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff00c7dd-8c79-4c11-a85b-a945ab530d01/dqc_reference/reference_markers_gtdb.fasta -out GCA_022720115.1_ASM2272011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:24:43,570] [INFO] Task succeeded: Blastn
[2023-06-13 00:24:43,575] [INFO] Selected 14 target genomes.
[2023-06-13 00:24:43,575] [INFO] Target genome list was writen to GCA_022720115.1_ASM2272011v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:24:43,581] [INFO] Task started: fastANI
[2023-06-13 00:24:43,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a646236-2756-43f4-ad4d-8835277004c5/GCA_022720115.1_ASM2272011v1_genomic.fna.gz --refList GCA_022720115.1_ASM2272011v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022720115.1_ASM2272011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:24:53,232] [INFO] Task succeeded: fastANI
[2023-06-13 00:24:53,255] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:24:53,255] [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_000012845.1	s__Parabacteroides distasonis	97.3085	577	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	conclusive
GCF_004793765.1	s__Parabacteroides distasonis_A	93.7359	472	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_011038785.1	s__Parabacteroides sp011038785	89.4354	394	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154105.1	s__Parabacteroides merdae	78.7018	148	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.8595	125	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.8189	132	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015550595.1	s__Parabacteroides sp900540715	77.8105	138	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCA_905196875.1	s__Parabacteroides sp905196875	77.7436	113	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156495.1	s__Parabacteroides johnsonii	77.6425	141	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_900770835.1	s__Parabacteroides sp900770835	77.5534	104	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.5464	142	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCA_900552465.1	s__Parabacteroides sp900552465	77.3238	117	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	76.9228	73	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-13 00:24:53,258] [INFO] GTDB search result was written to GCA_022720115.1_ASM2272011v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:24:53,259] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:24:53,262] [INFO] DFAST_QC result json was written to GCA_022720115.1_ASM2272011v1_genomic.fna/dqc_result.json
[2023-06-13 00:24:53,262] [INFO] DFAST_QC completed!
[2023-06-13 00:24:53,262] [INFO] Total running time: 0h1m29s