[2023-06-17 09:33:14,150] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:33:14,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:33:14,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference
[2023-06-17 09:33:15,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:33:15,974] [INFO] Task started: Prodigal
[2023-06-17 09:33:15,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg23e60aec-684b-49cb-b0db-f8274469e8b1/GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna.gz | prodigal -d GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/cds.fna -a GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:33:23,294] [INFO] Task succeeded: Prodigal
[2023-06-17 09:33:23,294] [INFO] Task started: HMMsearch
[2023-06-17 09:33:23,295] [INFO] Running command: hmmsearch --tblout GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference/reference_markers.hmm GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:33:23,491] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:33:23,493] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg23e60aec-684b-49cb-b0db-f8274469e8b1/GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna.gz]
[2023-06-17 09:33:23,520] [INFO] Query marker FASTA was written to GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/markers.fasta
[2023-06-17 09:33:23,520] [INFO] Task started: Blastn
[2023-06-17 09:33:23,520] [INFO] Running command: blastn -query GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference/reference_markers.fasta -out GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:33:24,194] [INFO] Task succeeded: Blastn
[2023-06-17 09:33:24,199] [INFO] Selected 11 target genomes.
[2023-06-17 09:33:24,200] [INFO] Target genome list was writen to GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/target_genomes.txt
[2023-06-17 09:33:24,203] [INFO] Task started: fastANI
[2023-06-17 09:33:24,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg23e60aec-684b-49cb-b0db-f8274469e8b1/GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna.gz --refList GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/target_genomes.txt --output GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:33:31,084] [INFO] Task succeeded: fastANI
[2023-06-17 09:33:31,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:33:31,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:33:31,100] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-06-17 09:33:31,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 09:33:31,100] [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	98.6882	650	707	95	conclusive
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	98.6553	644	707	95	conclusive
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	92.8645	578	707	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	84.0751	450	707	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	83.8897	445	707	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	83.6491	409	707	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	83.6251	407	707	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	83.5866	410	707	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	83.4478	424	707	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	82.7964	413	707	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	82.6923	423	707	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 09:33:31,103] [INFO] DFAST Taxonomy check result was written to GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/tc_result.tsv
[2023-06-17 09:33:31,103] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:33:31,104] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:33:31,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference/checkm_data
[2023-06-17 09:33:31,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:33:31,140] [INFO] Task started: CheckM
[2023-06-17 09:33:31,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/checkm_input GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/checkm_result
[2023-06-17 09:33:56,312] [INFO] Task succeeded: CheckM
[2023-06-17 09:33:56,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:33:56,332] [INFO] ===== Completeness check finished =====
[2023-06-17 09:33:56,333] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:33:56,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/markers.fasta)
[2023-06-17 09:33:56,334] [INFO] Task started: Blastn
[2023-06-17 09:33:56,334] [INFO] Running command: blastn -query GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ead0bdb-e5ab-4855-b8cd-a69b73133e01/dqc_reference/reference_markers_gtdb.fasta -out GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:33:57,366] [INFO] Task succeeded: Blastn
[2023-06-17 09:33:57,382] [INFO] Selected 10 target genomes.
[2023-06-17 09:33:57,383] [INFO] Target genome list was writen to GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:33:57,388] [INFO] Task started: fastANI
[2023-06-17 09:33:57,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg23e60aec-684b-49cb-b0db-f8274469e8b1/GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna.gz --refList GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/target_genomes_gtdb.txt --output GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:34:04,116] [INFO] Task succeeded: fastANI
[2023-06-17 09:34:04,129] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 09:34:04,129] [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_900199375.1	s__Gordonibacter urolithinfaciens	98.6882	650	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	conclusive
GCF_000210055.1	s__Gordonibacter pamelaeae	92.8645	578	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCA_900170005.1	s__Gordonibacter massiliensis	86.3289	563	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCF_003339845.1	s__Gordonibacter sp003339845	86.124	550	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009834925.2	s__Eggerthella sp014287365	84.0171	453	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_900184265.1	s__Eggerthella timonensis	83.9106	444	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024265.1	s__Eggerthella lenta	83.5066	421	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_002899715.1	s__Enteroscipio rubneri	83.1174	338	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Enteroscipio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003339815.1	s__Eggerthella sinensis	82.756	419	707	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-17 09:34:04,131] [INFO] GTDB search result was written to GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/result_gtdb.tsv
[2023-06-17 09:34:04,131] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:34:04,135] [INFO] DFAST_QC result json was written to GCA_905203085.1_ERR260135-mag-bin.48_genomic.fna/dqc_result.json
[2023-06-17 09:34:04,135] [INFO] DFAST_QC completed!
[2023-06-17 09:34:04,135] [INFO] Total running time: 0h0m50s