[2024-01-24 12:14:09,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,882] [INFO] DQC Reference Directory: /var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference
[2024-01-24 12:14:11,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,221] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,221] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc1f95c2-024e-4634-be5c-80e3834b7115/GCF_024158025.1_ASM2415802v1_genomic.fna.gz | prodigal -d GCF_024158025.1_ASM2415802v1_genomic.fna/cds.fna -a GCF_024158025.1_ASM2415802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:50,940] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:50,940] [INFO] Task started: HMMsearch
[2024-01-24 12:14:50,940] [INFO] Running command: hmmsearch --tblout GCF_024158025.1_ASM2415802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference/reference_markers.hmm GCF_024158025.1_ASM2415802v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:51,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:51,318] [INFO] Found 6/6 markers.
[2024-01-24 12:14:51,383] [INFO] Query marker FASTA was written to GCF_024158025.1_ASM2415802v1_genomic.fna/markers.fasta
[2024-01-24 12:14:51,384] [INFO] Task started: Blastn
[2024-01-24 12:14:51,384] [INFO] Running command: blastn -query GCF_024158025.1_ASM2415802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference/reference_markers.fasta -out GCF_024158025.1_ASM2415802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:52,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:52,030] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:52,031] [INFO] Target genome list was writen to GCF_024158025.1_ASM2415802v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:52,035] [INFO] Task started: fastANI
[2024-01-24 12:14:52,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1f95c2-024e-4634-be5c-80e3834b7115/GCF_024158025.1_ASM2415802v1_genomic.fna.gz --refList GCF_024158025.1_ASM2415802v1_genomic.fna/target_genomes.txt --output GCF_024158025.1_ASM2415802v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:05,917] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:05,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:05,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:05,930] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:05,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:05,931] [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 aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	93.5503	1969	2331	95	below_threshold
Runella rosea	strain=HYN0085	GCA_003325355.1	2259595	2259595	type	True	92.1718	1967	2331	95	below_threshold
Runella slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	81.5103	1336	2331	95	below_threshold
Runella zeae	strain=DSM 19591	GCA_000423565.1	94255	94255	type	True	77.6884	633	2331	95	below_threshold
Runella defluvii	strain=DSM 17976	GCA_014195535.1	370973	370973	type	True	77.6138	657	2331	95	below_threshold
Runella limosa	strain=DSM 17973	GCA_000482465.1	370978	370978	type	True	77.5103	640	2331	95	below_threshold
Persicitalea jodogahamensis	strain=KCTC 12866	GCA_014651615.1	402147	402147	type	True	75.1793	54	2331	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	75.0823	84	2331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,933] [INFO] DFAST Taxonomy check result was written to GCF_024158025.1_ASM2415802v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:05,934] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:05,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:05,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference/checkm_data
[2024-01-24 12:15:05,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:05,999] [INFO] Task started: CheckM
[2024-01-24 12:15:06,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024158025.1_ASM2415802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024158025.1_ASM2415802v1_genomic.fna/checkm_input GCF_024158025.1_ASM2415802v1_genomic.fna/checkm_result
[2024-01-24 12:16:45,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:45,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:45,693] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:45,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:45,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024158025.1_ASM2415802v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:45,694] [INFO] Task started: Blastn
[2024-01-24 12:16:45,694] [INFO] Running command: blastn -query GCF_024158025.1_ASM2415802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf32c2f07-0c72-4935-be26-e79b97983a96/dqc_reference/reference_markers_gtdb.fasta -out GCF_024158025.1_ASM2415802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:46,418] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:46,423] [INFO] Selected 9 target genomes.
[2024-01-24 12:16:46,423] [INFO] Target genome list was writen to GCF_024158025.1_ASM2415802v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:46,449] [INFO] Task started: fastANI
[2024-01-24 12:16:46,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1f95c2-024e-4634-be5c-80e3834b7115/GCF_024158025.1_ASM2415802v1_genomic.fna.gz --refList GCF_024158025.1_ASM2415802v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024158025.1_ASM2415802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:00,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:00,620] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:00,620] [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_009905605.1	s__Runella sp009905605	95.8857	2017	2331	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_003339505.1	s__Runella sp003339505	93.5553	1969	2331	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	92.1718	1967	2331	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	81.5157	1335	2331	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	77.8123	640	2331	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	77.6926	634	2331	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	77.6188	656	2331	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	77.5033	640	2331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727875.1	s__Larkinella sp008727875	75.0824	84	2331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:00,622] [INFO] GTDB search result was written to GCF_024158025.1_ASM2415802v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:00,622] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:00,625] [INFO] DFAST_QC result json was written to GCF_024158025.1_ASM2415802v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:00,625] [INFO] DFAST_QC completed!
[2024-01-24 12:17:00,625] [INFO] Total running time: 0h2m51s