[2023-06-17 11:08:12,913] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:08:12,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:08:12,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference
[2023-06-17 11:08:14,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:08:14,212] [INFO] Task started: Prodigal
[2023-06-17 11:08:14,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f4cbe79-12d0-44c8-840a-0e695f088609/GCA_028708075.1_ASM2870807v1_genomic.fna.gz | prodigal -d GCA_028708075.1_ASM2870807v1_genomic.fna/cds.fna -a GCA_028708075.1_ASM2870807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:08:28,311] [INFO] Task succeeded: Prodigal
[2023-06-17 11:08:28,312] [INFO] Task started: HMMsearch
[2023-06-17 11:08:28,312] [INFO] Running command: hmmsearch --tblout GCA_028708075.1_ASM2870807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference/reference_markers.hmm GCA_028708075.1_ASM2870807v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:08:28,585] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:08:28,587] [INFO] Found 6/6 markers.
[2023-06-17 11:08:28,621] [INFO] Query marker FASTA was written to GCA_028708075.1_ASM2870807v1_genomic.fna/markers.fasta
[2023-06-17 11:08:28,622] [INFO] Task started: Blastn
[2023-06-17 11:08:28,622] [INFO] Running command: blastn -query GCA_028708075.1_ASM2870807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference/reference_markers.fasta -out GCA_028708075.1_ASM2870807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:29,238] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:29,244] [INFO] Selected 26 target genomes.
[2023-06-17 11:08:29,245] [INFO] Target genome list was writen to GCA_028708075.1_ASM2870807v1_genomic.fna/target_genomes.txt
[2023-06-17 11:08:29,248] [INFO] Task started: fastANI
[2023-06-17 11:08:29,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f4cbe79-12d0-44c8-840a-0e695f088609/GCA_028708075.1_ASM2870807v1_genomic.fna.gz --refList GCA_028708075.1_ASM2870807v1_genomic.fna/target_genomes.txt --output GCA_028708075.1_ASM2870807v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:08:47,614] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:47,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:08:47,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:08:47,625] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:08:47,625] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:08:47,625] [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
Massilibacteroides vaginae	strain=MV12	GCA_900178525.1	1673718	1673718	type	True	77.6667	231	1028	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	76.9951	98	1028	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	76.9446	119	1028	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	76.9292	99	1028	95	below_threshold
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	76.9216	116	1028	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	76.8658	94	1028	95	below_threshold
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	76.823	98	1028	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	76.7427	92	1028	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	76.7391	90	1028	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	76.713	99	1028	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:08:47,628] [INFO] DFAST Taxonomy check result was written to GCA_028708075.1_ASM2870807v1_genomic.fna/tc_result.tsv
[2023-06-17 11:08:47,629] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:08:47,629] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:08:47,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference/checkm_data
[2023-06-17 11:08:47,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:08:47,670] [INFO] Task started: CheckM
[2023-06-17 11:08:47,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708075.1_ASM2870807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708075.1_ASM2870807v1_genomic.fna/checkm_input GCA_028708075.1_ASM2870807v1_genomic.fna/checkm_result
[2023-06-17 11:09:30,695] [INFO] Task succeeded: CheckM
[2023-06-17 11:09:30,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:09:30,717] [INFO] ===== Completeness check finished =====
[2023-06-17 11:09:30,718] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:09:30,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708075.1_ASM2870807v1_genomic.fna/markers.fasta)
[2023-06-17 11:09:30,718] [INFO] Task started: Blastn
[2023-06-17 11:09:30,719] [INFO] Running command: blastn -query GCA_028708075.1_ASM2870807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg762f90d3-d9eb-40b2-bea2-1db7e46474c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708075.1_ASM2870807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:09:31,501] [INFO] Task succeeded: Blastn
[2023-06-17 11:09:31,506] [INFO] Selected 29 target genomes.
[2023-06-17 11:09:31,507] [INFO] Target genome list was writen to GCA_028708075.1_ASM2870807v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:09:31,539] [INFO] Task started: fastANI
[2023-06-17 11:09:31,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f4cbe79-12d0-44c8-840a-0e695f088609/GCA_028708075.1_ASM2870807v1_genomic.fna.gz --refList GCA_028708075.1_ASM2870807v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708075.1_ASM2870807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:09:48,123] [INFO] Task succeeded: fastANI
[2023-06-17 11:09:48,142] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 11:09:48,143] [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_900178525.1	s__Massilibacteroides vaginae	77.6667	231	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Massilibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162725.1	s__Marseille-P3160 sp900162725	77.3508	74	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Marseille-P3160	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500925.1	s__Barb7 sp010500925	77.1206	73	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Barb7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108035.1	s__Parabacteroides chinchillae	76.9227	93	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	-
GCF_015550595.1	s__Parabacteroides sp900540715	76.8787	111	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_003473295.1	s__Parabacteroides sp003473295	76.8486	105	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015060925.1	s__Parabacteroides distasonis_B	76.8207	62	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.66	98.66	0.86	0.86	2	-
GCA_900760525.1	s__Parabacteroides sp900760525	76.8112	75	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_000154105.1	s__Parabacteroides merdae	76.7791	99	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCA_900541965.1	s__Parabacteroides sp900541965	76.7666	92	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.98	99.95	0.94	0.89	3	-
GCF_003363715.1	s__Parabacteroides acidifaciens	76.7408	91	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCA_000436495.1	s__Parabacteroides faecavium	76.6822	58	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.87	96.42	0.81	0.77	5	-
GCA_910577325.1	s__Parabacteroides sp910577325	76.6191	84	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552465.1	s__Parabacteroides sp900552465	76.0467	71	1028	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-17 11:09:48,145] [INFO] GTDB search result was written to GCA_028708075.1_ASM2870807v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:09:48,146] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:09:48,151] [INFO] DFAST_QC result json was written to GCA_028708075.1_ASM2870807v1_genomic.fna/dqc_result.json
[2023-06-17 11:09:48,151] [INFO] DFAST_QC completed!
[2023-06-17 11:09:48,151] [INFO] Total running time: 0h1m35s