[2024-01-25 19:11:35,463] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:35,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:35,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference
[2024-01-25 19:11:36,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:36,587] [INFO] Task started: Prodigal
[2024-01-25 19:11:36,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg129291ae-0e3c-4c5c-aa8a-2a14011a4a26/GCF_000218895.1_ASM21889v1_genomic.fna.gz | prodigal -d GCF_000218895.1_ASM21889v1_genomic.fna/cds.fna -a GCF_000218895.1_ASM21889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:07,015] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:07,015] [INFO] Task started: HMMsearch
[2024-01-25 19:12:07,016] [INFO] Running command: hmmsearch --tblout GCF_000218895.1_ASM21889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference/reference_markers.hmm GCF_000218895.1_ASM21889v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:07,354] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:07,356] [INFO] Found 6/6 markers.
[2024-01-25 19:12:07,425] [INFO] Query marker FASTA was written to GCF_000218895.1_ASM21889v1_genomic.fna/markers.fasta
[2024-01-25 19:12:07,425] [INFO] Task started: Blastn
[2024-01-25 19:12:07,425] [INFO] Running command: blastn -query GCF_000218895.1_ASM21889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference/reference_markers.fasta -out GCF_000218895.1_ASM21889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:07,978] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:07,981] [INFO] Selected 13 target genomes.
[2024-01-25 19:12:07,981] [INFO] Target genome list was writen to GCF_000218895.1_ASM21889v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:07,987] [INFO] Task started: fastANI
[2024-01-25 19:12:07,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg129291ae-0e3c-4c5c-aa8a-2a14011a4a26/GCF_000218895.1_ASM21889v1_genomic.fna.gz --refList GCF_000218895.1_ASM21889v1_genomic.fna/target_genomes.txt --output GCF_000218895.1_ASM21889v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:24,910] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:24,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:24,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:24,917] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:24,917] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:24,917] [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 slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	100.0	2303	2303	95	conclusive
Runella rosea	strain=HYN0085	GCA_003325355.1	2259595	2259595	type	True	81.6918	1385	2303	95	below_threshold
Runella aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	81.4305	1341	2303	95	below_threshold
Runella zeae	strain=DSM 19591	GCA_000423565.1	94255	94255	type	True	77.719	480	2303	95	below_threshold
Runella defluvii	strain=DSM 17976	GCA_014195535.1	370973	370973	type	True	77.6898	490	2303	95	below_threshold
Runella limosa	strain=DSM 17973	GCA_000482465.1	370978	370978	type	True	77.3959	467	2303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:24,918] [INFO] DFAST Taxonomy check result was written to GCF_000218895.1_ASM21889v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:24,919] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:24,919] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:24,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference/checkm_data
[2024-01-25 19:12:24,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:24,987] [INFO] Task started: CheckM
[2024-01-25 19:12:24,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000218895.1_ASM21889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000218895.1_ASM21889v1_genomic.fna/checkm_input GCF_000218895.1_ASM21889v1_genomic.fna/checkm_result
[2024-01-25 19:13:47,534] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:47,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:47,551] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:47,551] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:47,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000218895.1_ASM21889v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:47,552] [INFO] Task started: Blastn
[2024-01-25 19:13:47,552] [INFO] Running command: blastn -query GCF_000218895.1_ASM21889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d388c36-c851-41ca-ae73-dfe6afb24e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_000218895.1_ASM21889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:48,300] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:48,307] [INFO] Selected 11 target genomes.
[2024-01-25 19:13:48,307] [INFO] Target genome list was writen to GCF_000218895.1_ASM21889v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:48,321] [INFO] Task started: fastANI
[2024-01-25 19:13:48,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg129291ae-0e3c-4c5c-aa8a-2a14011a4a26/GCF_000218895.1_ASM21889v1_genomic.fna.gz --refList GCF_000218895.1_ASM21889v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000218895.1_ASM21889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:02,489] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:02,495] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:02,495] [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_000218895.1	s__Runella slithyformis	100.0	2303	2303	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_003325355.1	s__Runella sp003325355	81.6939	1384	2303	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	81.5204	1413	2303	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	81.4305	1341	2303	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	77.719	480	2303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	99.21	99.21	0.93	0.93	2	-
GCF_014195535.1	s__Runella defluvii	77.696	489	2303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	95.53	95.36	0.92	0.90	3	-
GCF_000482465.1	s__Runella limosa	77.4015	464	2303	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 19:14:02,497] [INFO] GTDB search result was written to GCF_000218895.1_ASM21889v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:02,497] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:02,499] [INFO] DFAST_QC result json was written to GCF_000218895.1_ASM21889v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:02,499] [INFO] DFAST_QC completed!
[2024-01-25 19:14:02,500] [INFO] Total running time: 0h2m27s