[2024-01-25 17:42:20,566] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference
[2024-01-25 17:42:21,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,686] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg520a6966-ad62-4e62-9544-b68b32292b17/GCF_000482465.1_ASM48246v1_genomic.fna.gz | prodigal -d GCF_000482465.1_ASM48246v1_genomic.fna/cds.fna -a GCF_000482465.1_ASM48246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:56,142] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:56,142] [INFO] Task started: HMMsearch
[2024-01-25 17:42:56,142] [INFO] Running command: hmmsearch --tblout GCF_000482465.1_ASM48246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference/reference_markers.hmm GCF_000482465.1_ASM48246v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:56,451] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:56,452] [INFO] Found 6/6 markers.
[2024-01-25 17:42:56,508] [INFO] Query marker FASTA was written to GCF_000482465.1_ASM48246v1_genomic.fna/markers.fasta
[2024-01-25 17:42:56,508] [INFO] Task started: Blastn
[2024-01-25 17:42:56,508] [INFO] Running command: blastn -query GCF_000482465.1_ASM48246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference/reference_markers.fasta -out GCF_000482465.1_ASM48246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:57,051] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:57,054] [INFO] Selected 14 target genomes.
[2024-01-25 17:42:57,054] [INFO] Target genome list was writen to GCF_000482465.1_ASM48246v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:57,061] [INFO] Task started: fastANI
[2024-01-25 17:42:57,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg520a6966-ad62-4e62-9544-b68b32292b17/GCF_000482465.1_ASM48246v1_genomic.fna.gz --refList GCF_000482465.1_ASM48246v1_genomic.fna/target_genomes.txt --output GCF_000482465.1_ASM48246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:14,641] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:14,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:14,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:14,648] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:14,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:14,649] [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 limosa	strain=DSM 17973	GCA_000482465.1	370978	370978	type	True	100.0	2467	2481	95	conclusive
Runella defluvii	strain=DSM 17976	GCA_014195535.1	370973	370973	type	True	91.4386	2032	2481	95	below_threshold
Runella zeae	strain=DSM 19591	GCA_000423565.1	94255	94255	type	True	79.303	651	2481	95	below_threshold
Runella rosea	strain=HYN0085	GCA_003325355.1	2259595	2259595	type	True	77.4946	621	2481	95	below_threshold
Runella slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	77.4601	470	2481	95	below_threshold
Runella aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	77.4566	631	2481	95	below_threshold
Flectobacillus major	strain=DSM 103	GCA_000427405.1	103	103	type	True	75.9666	84	2481	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	75.3585	61	2481	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	75.0702	64	2481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:14,650] [INFO] DFAST Taxonomy check result was written to GCF_000482465.1_ASM48246v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:14,650] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:14,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:14,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference/checkm_data
[2024-01-25 17:43:14,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:14,717] [INFO] Task started: CheckM
[2024-01-25 17:43:14,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482465.1_ASM48246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482465.1_ASM48246v1_genomic.fna/checkm_input GCF_000482465.1_ASM48246v1_genomic.fna/checkm_result
[2024-01-25 17:44:47,857] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:47,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:47,877] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:47,877] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:47,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482465.1_ASM48246v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:47,878] [INFO] Task started: Blastn
[2024-01-25 17:44:47,878] [INFO] Running command: blastn -query GCF_000482465.1_ASM48246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45926b12-1317-4b95-a996-8c31a9c80a75/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482465.1_ASM48246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:48,699] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:48,701] [INFO] Selected 11 target genomes.
[2024-01-25 17:44:48,701] [INFO] Target genome list was writen to GCF_000482465.1_ASM48246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:48,717] [INFO] Task started: fastANI
[2024-01-25 17:44:48,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg520a6966-ad62-4e62-9544-b68b32292b17/GCF_000482465.1_ASM48246v1_genomic.fna.gz --refList GCF_000482465.1_ASM48246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482465.1_ASM48246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:04,251] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:04,257] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:04,257] [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_000482465.1	s__Runella limosa	100.0	2467	2481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014195535.1	s__Runella defluvii	91.4238	2034	2481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	95.53	95.36	0.92	0.90	3	-
GCF_003711225.1	s__Runella sp003711225	90.151	1978	2481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423565.1	s__Runella zeae	79.3193	647	2481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	99.21	99.21	0.93	0.93	2	-
GCF_003325355.1	s__Runella sp003325355	77.4979	623	2481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218895.1	s__Runella slithyformis	77.4566	470	2481	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	77.4531	631	2481	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	77.3556	631	2481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:04,264] [INFO] GTDB search result was written to GCF_000482465.1_ASM48246v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:04,264] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:04,267] [INFO] DFAST_QC result json was written to GCF_000482465.1_ASM48246v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:04,267] [INFO] DFAST_QC completed!
[2024-01-25 17:45:04,267] [INFO] Total running time: 0h2m44s