[2023-06-29 13:25:59,824] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:25:59,827] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:25:59,827] [INFO] DQC Reference Directory: /var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference
[2023-06-29 13:26:01,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:26:01,031] [INFO] Task started: Prodigal
[2023-06-29 13:26:01,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg9290d7bd-3741-445f-b277-17f6e5be6ea3/GCA_023413405.1_ASM2341340v1_genomic.fna.gz | prodigal -d GCA_023413405.1_ASM2341340v1_genomic.fna/cds.fna -a GCA_023413405.1_ASM2341340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:26:15,256] [INFO] Task succeeded: Prodigal
[2023-06-29 13:26:15,257] [INFO] Task started: HMMsearch
[2023-06-29 13:26:15,257] [INFO] Running command: hmmsearch --tblout GCA_023413405.1_ASM2341340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference/reference_markers.hmm GCA_023413405.1_ASM2341340v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:26:15,461] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:26:15,462] [INFO] Found 6/6 markers.
[2023-06-29 13:26:15,490] [INFO] Query marker FASTA was written to GCA_023413405.1_ASM2341340v1_genomic.fna/markers.fasta
[2023-06-29 13:26:15,491] [INFO] Task started: Blastn
[2023-06-29 13:26:15,491] [INFO] Running command: blastn -query GCA_023413405.1_ASM2341340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference/reference_markers.fasta -out GCA_023413405.1_ASM2341340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:26:16,086] [INFO] Task succeeded: Blastn
[2023-06-29 13:26:16,090] [INFO] Selected 12 target genomes.
[2023-06-29 13:26:16,090] [INFO] Target genome list was writen to GCA_023413405.1_ASM2341340v1_genomic.fna/target_genomes.txt
[2023-06-29 13:26:16,093] [INFO] Task started: fastANI
[2023-06-29 13:26:16,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg9290d7bd-3741-445f-b277-17f6e5be6ea3/GCA_023413405.1_ASM2341340v1_genomic.fna.gz --refList GCA_023413405.1_ASM2341340v1_genomic.fna/target_genomes.txt --output GCA_023413405.1_ASM2341340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:26:25,185] [INFO] Task succeeded: fastANI
[2023-06-29 13:26:25,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:26:25,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:26:25,197] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-29 13:26:25,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 13:26:25,197] [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=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	98.6578	859	898	95	conclusive
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	98.6351	859	898	95	conclusive
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	98.626	859	898	95	conclusive
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	78.2049	266	898	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	78.1896	254	898	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	78.1793	254	898	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	77.9727	263	898	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	77.9695	263	898	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	77.9355	253	898	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:26:25,200] [INFO] DFAST Taxonomy check result was written to GCA_023413405.1_ASM2341340v1_genomic.fna/tc_result.tsv
[2023-06-29 13:26:25,201] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:26:25,201] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:26:25,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference/checkm_data
[2023-06-29 13:26:25,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:26:25,236] [INFO] Task started: CheckM
[2023-06-29 13:26:25,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023413405.1_ASM2341340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023413405.1_ASM2341340v1_genomic.fna/checkm_input GCA_023413405.1_ASM2341340v1_genomic.fna/checkm_result
[2023-06-29 13:27:07,823] [INFO] Task succeeded: CheckM
[2023-06-29 13:27:07,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:27:07,841] [INFO] ===== Completeness check finished =====
[2023-06-29 13:27:07,841] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:27:07,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023413405.1_ASM2341340v1_genomic.fna/markers.fasta)
[2023-06-29 13:27:07,842] [INFO] Task started: Blastn
[2023-06-29 13:27:07,842] [INFO] Running command: blastn -query GCA_023413405.1_ASM2341340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge82093ca-1382-4a9c-8e82-06741db526c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_023413405.1_ASM2341340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:27:08,629] [INFO] Task succeeded: Blastn
[2023-06-29 13:27:08,633] [INFO] Selected 15 target genomes.
[2023-06-29 13:27:08,633] [INFO] Target genome list was writen to GCA_023413405.1_ASM2341340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:27:08,641] [INFO] Task started: fastANI
[2023-06-29 13:27:08,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg9290d7bd-3741-445f-b277-17f6e5be6ea3/GCA_023413405.1_ASM2341340v1_genomic.fna.gz --refList GCA_023413405.1_ASM2341340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023413405.1_ASM2341340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:27:19,560] [INFO] Task succeeded: fastANI
[2023-06-29 13:27:19,571] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:27:19,572] [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	98.626	859	898	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	94.5031	689	898	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	90.4189	585	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905196875.1	s__Parabacteroides sp905196875	78.2915	223	898	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	78.2356	256	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_003363715.1	s__Parabacteroides acidifaciens	78.1967	251	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	78.0503	249	898	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	77.9811	260	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.8922	237	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_014287585.1	s__Parabacteroides sp014287585	77.8468	279	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_900552465.1	s__Parabacteroides sp900552465	77.6429	228	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCA_900770835.1	s__Parabacteroides sp900770835	77.5167	174	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	77.427	115	898	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-29 13:27:19,574] [INFO] GTDB search result was written to GCA_023413405.1_ASM2341340v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:27:19,574] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:27:19,577] [INFO] DFAST_QC result json was written to GCA_023413405.1_ASM2341340v1_genomic.fna/dqc_result.json
[2023-06-29 13:27:19,578] [INFO] DFAST_QC completed!
[2023-06-29 13:27:19,578] [INFO] Total running time: 0h1m20s