[2023-06-04 20:24:01,882] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:01,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:01,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference
[2023-06-04 20:24:03,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:03,369] [INFO] Task started: Prodigal
[2023-06-04 20:24:03,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg92f1f730-b93c-4d28-b80a-26341770d887/GCA_004293985.1_ASM429398v1_genomic.fna.gz | prodigal -d GCA_004293985.1_ASM429398v1_genomic.fna/cds.fna -a GCA_004293985.1_ASM429398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:23,250] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:23,250] [INFO] Task started: HMMsearch
[2023-06-04 20:24:23,250] [INFO] Running command: hmmsearch --tblout GCA_004293985.1_ASM429398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference/reference_markers.hmm GCA_004293985.1_ASM429398v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:23,511] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:23,512] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg92f1f730-b93c-4d28-b80a-26341770d887/GCA_004293985.1_ASM429398v1_genomic.fna.gz]
[2023-06-04 20:24:23,546] [INFO] Query marker FASTA was written to GCA_004293985.1_ASM429398v1_genomic.fna/markers.fasta
[2023-06-04 20:24:23,547] [INFO] Task started: Blastn
[2023-06-04 20:24:23,547] [INFO] Running command: blastn -query GCA_004293985.1_ASM429398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference/reference_markers.fasta -out GCA_004293985.1_ASM429398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:24,147] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:24,153] [INFO] Selected 17 target genomes.
[2023-06-04 20:24:24,154] [INFO] Target genome list was writen to GCA_004293985.1_ASM429398v1_genomic.fna/target_genomes.txt
[2023-06-04 20:24:24,163] [INFO] Task started: fastANI
[2023-06-04 20:24:24,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg92f1f730-b93c-4d28-b80a-26341770d887/GCA_004293985.1_ASM429398v1_genomic.fna.gz --refList GCA_004293985.1_ASM429398v1_genomic.fna/target_genomes.txt --output GCA_004293985.1_ASM429398v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:41,446] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:41,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:41,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:41,459] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:41,459] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:24:41,459] [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
Runella defluvii	strain=DSM 17976	GCA_014195535.1	370973	370973	type	True	76.6009	168	1010	95	below_threshold
Runella slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	76.3523	154	1010	95	below_threshold
Runella limosa	strain=DSM 17973	GCA_000482465.1	370978	370978	type	True	76.1651	145	1010	95	below_threshold
Runella aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	75.9976	169	1010	95	below_threshold
Runella rosea	strain=HYN0085	GCA_003325355.1	2259595	2259595	type	True	75.9893	151	1010	95	below_threshold
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	75.4881	56	1010	95	below_threshold
Rudanella lutea	strain=DSM 19387	GCA_000383955.1	451374	451374	type	True	75.3881	58	1010	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:24:41,461] [INFO] DFAST Taxonomy check result was written to GCA_004293985.1_ASM429398v1_genomic.fna/tc_result.tsv
[2023-06-04 20:24:41,462] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:41,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:41,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference/checkm_data
[2023-06-04 20:24:41,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:41,501] [INFO] Task started: CheckM
[2023-06-04 20:24:41,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004293985.1_ASM429398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004293985.1_ASM429398v1_genomic.fna/checkm_input GCA_004293985.1_ASM429398v1_genomic.fna/checkm_result
[2023-06-04 20:25:35,018] [INFO] Task succeeded: CheckM
[2023-06-04 20:25:35,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:25:35,041] [INFO] ===== Completeness check finished =====
[2023-06-04 20:25:35,041] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:25:35,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004293985.1_ASM429398v1_genomic.fna/markers.fasta)
[2023-06-04 20:25:35,042] [INFO] Task started: Blastn
[2023-06-04 20:25:35,042] [INFO] Running command: blastn -query GCA_004293985.1_ASM429398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc1724e-0348-4031-9ed9-d82fe4aa807b/dqc_reference/reference_markers_gtdb.fasta -out GCA_004293985.1_ASM429398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:25:35,789] [INFO] Task succeeded: Blastn
[2023-06-04 20:25:35,795] [INFO] Selected 20 target genomes.
[2023-06-04 20:25:35,795] [INFO] Target genome list was writen to GCA_004293985.1_ASM429398v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:25:35,857] [INFO] Task started: fastANI
[2023-06-04 20:25:35,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg92f1f730-b93c-4d28-b80a-26341770d887/GCA_004293985.1_ASM429398v1_genomic.fna.gz --refList GCA_004293985.1_ASM429398v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004293985.1_ASM429398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:25:52,589] [INFO] Task succeeded: fastANI
[2023-06-04 20:25:52,602] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:25:52,603] [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
GCA_004293645.1	s__REAB01 sp004293645	98.3684	857	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__REAB01	95.0	99.03	98.31	0.91	0.83	11	conclusive
GCF_014195535.1	s__Runella defluvii	76.6009	168	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	95.53	95.36	0.92	0.90	3	-
GCA_013298215.1	s__JAAFKE01 sp013298215	76.5987	166	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__JAAFKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218895.1	s__Runella slithyformis	76.3523	154	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905605.1	s__Runella sp009905605	76.2472	142	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711225.1	s__Runella sp003711225	76.1037	152	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339505.1	s__Runella sp003339505	75.9976	169	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325355.1	s__Runella sp003325355	75.9893	151	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292855.1	s__Rudanella sp004292855	75.5328	64	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	98.31	98.31	0.91	0.91	2	-
GCF_000383955.1	s__Rudanella lutea	75.3881	58	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:25:52,605] [INFO] GTDB search result was written to GCA_004293985.1_ASM429398v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:25:52,605] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:25:52,610] [INFO] DFAST_QC result json was written to GCA_004293985.1_ASM429398v1_genomic.fna/dqc_result.json
[2023-06-04 20:25:52,610] [INFO] DFAST_QC completed!
[2023-06-04 20:25:52,610] [INFO] Total running time: 0h1m51s