[2024-01-25 19:43:50,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference
[2024-01-25 19:43:51,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,602] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgcee4478b-3730-41c8-8bee-18fb62e1d0e4/GCF_003340105.1_ASM334010v1_genomic.fna.gz | prodigal -d GCF_003340105.1_ASM334010v1_genomic.fna/cds.fna -a GCF_003340105.1_ASM334010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:01,489] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:01,489] [INFO] Task started: HMMsearch
[2024-01-25 19:44:01,489] [INFO] Running command: hmmsearch --tblout GCF_003340105.1_ASM334010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference/reference_markers.hmm GCF_003340105.1_ASM334010v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:01,698] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:01,699] [INFO] Found 6/6 markers.
[2024-01-25 19:44:01,729] [INFO] Query marker FASTA was written to GCF_003340105.1_ASM334010v1_genomic.fna/markers.fasta
[2024-01-25 19:44:01,730] [INFO] Task started: Blastn
[2024-01-25 19:44:01,730] [INFO] Running command: blastn -query GCF_003340105.1_ASM334010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference/reference_markers.fasta -out GCF_003340105.1_ASM334010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:02,424] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:02,426] [INFO] Selected 6 target genomes.
[2024-01-25 19:44:02,427] [INFO] Target genome list was writen to GCF_003340105.1_ASM334010v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:02,428] [INFO] Task started: fastANI
[2024-01-25 19:44:02,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgcee4478b-3730-41c8-8bee-18fb62e1d0e4/GCF_003340105.1_ASM334010v1_genomic.fna.gz --refList GCF_003340105.1_ASM334010v1_genomic.fna/target_genomes.txt --output GCF_003340105.1_ASM334010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:08,502] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:08,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:08,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:08,508] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:44:08,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:08,508] [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=ATCC 25559	GCA_003340105.1	84112	84112	type	True	100.0	1164	1165	95	conclusive
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	99.9983	1164	1165	95	conclusive
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	99.9968	1164	1165	95	conclusive
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	99.9967	1164	1165	95	conclusive
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	90.4196	894	1165	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	88.8144	863	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:08,509] [INFO] DFAST Taxonomy check result was written to GCF_003340105.1_ASM334010v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:08,510] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:08,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:08,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference/checkm_data
[2024-01-25 19:44:08,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:08,558] [INFO] Task started: CheckM
[2024-01-25 19:44:08,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003340105.1_ASM334010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003340105.1_ASM334010v1_genomic.fna/checkm_input GCF_003340105.1_ASM334010v1_genomic.fna/checkm_result
[2024-01-25 19:44:39,457] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:39,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:39,488] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:39,489] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:39,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003340105.1_ASM334010v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:39,489] [INFO] Task started: Blastn
[2024-01-25 19:44:39,489] [INFO] Running command: blastn -query GCF_003340105.1_ASM334010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03abb768-28ae-48b6-8c0e-af7d8a3075ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003340105.1_ASM334010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:40,772] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:40,774] [INFO] Selected 8 target genomes.
[2024-01-25 19:44:40,775] [INFO] Target genome list was writen to GCF_003340105.1_ASM334010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:40,780] [INFO] Task started: fastANI
[2024-01-25 19:44:40,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgcee4478b-3730-41c8-8bee-18fb62e1d0e4/GCF_003340105.1_ASM334010v1_genomic.fna.gz --refList GCF_003340105.1_ASM334010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003340105.1_ASM334010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:47,255] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:47,261] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:47,261] [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	99.9968	1164	1165	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	90.4258	894	1165	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	88.8144	863	1165	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	86.6742	800	1165	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	84.3666	673	1165	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	83.8383	630	1165	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCF_003726035.1	s__Paraeggerthella hongkongensis	81.5189	533	1165	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	99.02	99.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:47,268] [INFO] GTDB search result was written to GCF_003340105.1_ASM334010v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:47,268] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:47,270] [INFO] DFAST_QC result json was written to GCF_003340105.1_ASM334010v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:47,271] [INFO] DFAST_QC completed!
[2024-01-25 19:44:47,271] [INFO] Total running time: 0h0m57s