[2023-06-29 23:53:03,052] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:53:03,055] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:53:03,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference
[2023-06-29 23:53:04,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:53:04,257] [INFO] Task started: Prodigal
[2023-06-29 23:53:04,258] [INFO] Running command: gunzip -c /var/lib/cwl/stga09eff61-6bf1-41ff-8d2a-76785ad30b99/GCA_008669155.1_ASM866915v1_genomic.fna.gz | prodigal -d GCA_008669155.1_ASM866915v1_genomic.fna/cds.fna -a GCA_008669155.1_ASM866915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:53:10,516] [INFO] Task succeeded: Prodigal
[2023-06-29 23:53:10,517] [INFO] Task started: HMMsearch
[2023-06-29 23:53:10,517] [INFO] Running command: hmmsearch --tblout GCA_008669155.1_ASM866915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference/reference_markers.hmm GCA_008669155.1_ASM866915v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:53:10,728] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:53:10,729] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga09eff61-6bf1-41ff-8d2a-76785ad30b99/GCA_008669155.1_ASM866915v1_genomic.fna.gz]
[2023-06-29 23:53:10,752] [INFO] Query marker FASTA was written to GCA_008669155.1_ASM866915v1_genomic.fna/markers.fasta
[2023-06-29 23:53:10,752] [INFO] Task started: Blastn
[2023-06-29 23:53:10,752] [INFO] Running command: blastn -query GCA_008669155.1_ASM866915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference/reference_markers.fasta -out GCA_008669155.1_ASM866915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:53:11,522] [INFO] Task succeeded: Blastn
[2023-06-29 23:53:11,527] [INFO] Selected 6 target genomes.
[2023-06-29 23:53:11,527] [INFO] Target genome list was writen to GCA_008669155.1_ASM866915v1_genomic.fna/target_genomes.txt
[2023-06-29 23:53:11,529] [INFO] Task started: fastANI
[2023-06-29 23:53:11,529] [INFO] Running command: fastANI --query /var/lib/cwl/stga09eff61-6bf1-41ff-8d2a-76785ad30b99/GCA_008669155.1_ASM866915v1_genomic.fna.gz --refList GCA_008669155.1_ASM866915v1_genomic.fna/target_genomes.txt --output GCA_008669155.1_ASM866915v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:53:15,704] [INFO] Task succeeded: fastANI
[2023-06-29 23:53:15,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:53:15,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:53:15,717] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2023-06-29 23:53:15,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 23:53:15,718] [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
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	98.2174	550	588	95	conclusive
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	98.2135	546	588	95	conclusive
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	98.1688	546	588	95	conclusive
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	98.1527	545	588	95	conclusive
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	89.4945	516	588	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	88.4818	518	588	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:53:15,720] [INFO] DFAST Taxonomy check result was written to GCA_008669155.1_ASM866915v1_genomic.fna/tc_result.tsv
[2023-06-29 23:53:15,721] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:53:15,721] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:53:15,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference/checkm_data
[2023-06-29 23:53:15,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:53:15,753] [INFO] Task started: CheckM
[2023-06-29 23:53:15,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008669155.1_ASM866915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008669155.1_ASM866915v1_genomic.fna/checkm_input GCA_008669155.1_ASM866915v1_genomic.fna/checkm_result
[2023-06-29 23:53:39,376] [INFO] Task succeeded: CheckM
[2023-06-29 23:53:39,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:53:39,399] [INFO] ===== Completeness check finished =====
[2023-06-29 23:53:39,400] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:53:39,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008669155.1_ASM866915v1_genomic.fna/markers.fasta)
[2023-06-29 23:53:39,401] [INFO] Task started: Blastn
[2023-06-29 23:53:39,401] [INFO] Running command: blastn -query GCA_008669155.1_ASM866915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd355d4-beb7-4c5f-96a8-68a27c43e1d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_008669155.1_ASM866915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:53:40,562] [INFO] Task succeeded: Blastn
[2023-06-29 23:53:40,567] [INFO] Selected 7 target genomes.
[2023-06-29 23:53:40,567] [INFO] Target genome list was writen to GCA_008669155.1_ASM866915v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:53:40,568] [INFO] Task started: fastANI
[2023-06-29 23:53:40,569] [INFO] Running command: fastANI --query /var/lib/cwl/stga09eff61-6bf1-41ff-8d2a-76785ad30b99/GCA_008669155.1_ASM866915v1_genomic.fna.gz --refList GCA_008669155.1_ASM866915v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008669155.1_ASM866915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:53:45,200] [INFO] Task succeeded: fastANI
[2023-06-29 23:53:45,211] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:53:45,211] [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_000024265.1	s__Eggerthella lenta	98.2174	550	588	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	conclusive
GCF_009834925.2	s__Eggerthella sp014287365	89.4662	517	588	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	88.4818	518	588	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339815.1	s__Eggerthella sinensis	86.3437	500	588	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCF_902386925.1	s__Arabia massiliensis	83.859	435	588	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003726035.1	s__Paraeggerthella hongkongensis	81.4035	336	588	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	99.02	99.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:53:45,213] [INFO] GTDB search result was written to GCA_008669155.1_ASM866915v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:53:45,213] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:53:45,216] [INFO] DFAST_QC result json was written to GCA_008669155.1_ASM866915v1_genomic.fna/dqc_result.json
[2023-06-29 23:53:45,216] [INFO] DFAST_QC completed!
[2023-06-29 23:53:45,216] [INFO] Total running time: 0h0m42s