[2024-01-24 12:13:38,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:38,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:38,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference
[2024-01-24 12:13:39,310] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:39,311] [INFO] Task started: Prodigal
[2024-01-24 12:13:39,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg2111f31b-d067-4435-a052-9b967e57f9de/GCF_002899715.1_ASM289971v1_genomic.fna.gz | prodigal -d GCF_002899715.1_ASM289971v1_genomic.fna/cds.fna -a GCF_002899715.1_ASM289971v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:48,429] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:48,430] [INFO] Task started: HMMsearch
[2024-01-24 12:13:48,430] [INFO] Running command: hmmsearch --tblout GCF_002899715.1_ASM289971v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference/reference_markers.hmm GCF_002899715.1_ASM289971v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:48,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:48,673] [INFO] Found 6/6 markers.
[2024-01-24 12:13:48,697] [INFO] Query marker FASTA was written to GCF_002899715.1_ASM289971v1_genomic.fna/markers.fasta
[2024-01-24 12:13:48,697] [INFO] Task started: Blastn
[2024-01-24 12:13:48,697] [INFO] Running command: blastn -query GCF_002899715.1_ASM289971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference/reference_markers.fasta -out GCF_002899715.1_ASM289971v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:49,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:49,334] [INFO] Selected 10 target genomes.
[2024-01-24 12:13:49,334] [INFO] Target genome list was writen to GCF_002899715.1_ASM289971v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:49,850] [INFO] Task started: fastANI
[2024-01-24 12:13:49,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg2111f31b-d067-4435-a052-9b967e57f9de/GCF_002899715.1_ASM289971v1_genomic.fna.gz --refList GCF_002899715.1_ASM289971v1_genomic.fna/target_genomes.txt --output GCF_002899715.1_ASM289971v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:56,291] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:56,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:56,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:56,301] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:13:56,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:13:56,301] [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
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	84.3137	519	924	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	84.2865	516	924	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	83.3185	539	924	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	82.9815	553	924	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	82.2132	488	924	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	82.1864	490	924	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	82.1776	499	924	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	82.1725	485	924	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	81.7621	507	924	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	81.7245	538	924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:56,305] [INFO] DFAST Taxonomy check result was written to GCF_002899715.1_ASM289971v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:56,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:56,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:56,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference/checkm_data
[2024-01-24 12:13:56,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:56,349] [INFO] Task started: CheckM
[2024-01-24 12:13:56,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002899715.1_ASM289971v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002899715.1_ASM289971v1_genomic.fna/checkm_input GCF_002899715.1_ASM289971v1_genomic.fna/checkm_result
[2024-01-24 12:14:27,145] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:27,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:27,171] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:27,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:27,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002899715.1_ASM289971v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:27,172] [INFO] Task started: Blastn
[2024-01-24 12:14:27,173] [INFO] Running command: blastn -query GCF_002899715.1_ASM289971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4705df-e948-4533-b054-297203b5da15/dqc_reference/reference_markers_gtdb.fasta -out GCF_002899715.1_ASM289971v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:28,188] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:28,192] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:28,192] [INFO] Target genome list was writen to GCF_002899715.1_ASM289971v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:28,206] [INFO] Task started: fastANI
[2024-01-24 12:14:28,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg2111f31b-d067-4435-a052-9b967e57f9de/GCF_002899715.1_ASM289971v1_genomic.fna.gz --refList GCF_002899715.1_ASM289971v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002899715.1_ASM289971v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:35,310] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:35,322] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:35,323] [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_002899715.1	s__Enteroscipio rubneri	100.0	922	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Enteroscipio	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_900199375.1	s__Gordonibacter urolithinfaciens	84.3518	517	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCF_900184265.1	s__Eggerthella timonensis	83.3599	536	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834925.2	s__Eggerthella sp014287365	82.9662	555	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_000024265.1	s__Eggerthella lenta	82.1161	503	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_003339815.1	s__Eggerthella sinensis	81.7244	538	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCF_002159915.1	s__Rubneribacter sp002159915	81.2667	418	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Rubneribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115845.1	s__Rubneribacter avistercoris	80.7789	379	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Rubneribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003726035.1	s__Paraeggerthella hongkongensis	80.1763	348	924	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	99.02	99.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:35,328] [INFO] GTDB search result was written to GCF_002899715.1_ASM289971v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:35,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:35,333] [INFO] DFAST_QC result json was written to GCF_002899715.1_ASM289971v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:35,333] [INFO] DFAST_QC completed!
[2024-01-24 12:14:35,333] [INFO] Total running time: 0h0m57s