[2024-01-24 11:26:39,345] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:39,346] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:39,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference
[2024-01-24 11:26:40,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,557] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,557] [INFO] Running command: gunzip -c /var/lib/cwl/stgb62dbbae-487a-4751-9e7b-7b42494da8f9/GCF_009834925.2_ASM983492v2_genomic.fna.gz | prodigal -d GCF_009834925.2_ASM983492v2_genomic.fna/cds.fna -a GCF_009834925.2_ASM983492v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:54,270] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:54,271] [INFO] Task started: HMMsearch
[2024-01-24 11:26:54,271] [INFO] Running command: hmmsearch --tblout GCF_009834925.2_ASM983492v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference/reference_markers.hmm GCF_009834925.2_ASM983492v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:54,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:54,565] [INFO] Found 6/6 markers.
[2024-01-24 11:26:54,605] [INFO] Query marker FASTA was written to GCF_009834925.2_ASM983492v2_genomic.fna/markers.fasta
[2024-01-24 11:26:54,606] [INFO] Task started: Blastn
[2024-01-24 11:26:54,606] [INFO] Running command: blastn -query GCF_009834925.2_ASM983492v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference/reference_markers.fasta -out GCF_009834925.2_ASM983492v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:55,380] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:55,391] [INFO] Selected 7 target genomes.
[2024-01-24 11:26:55,392] [INFO] Target genome list was writen to GCF_009834925.2_ASM983492v2_genomic.fna/target_genomes.txt
[2024-01-24 11:26:55,401] [INFO] Task started: fastANI
[2024-01-24 11:26:55,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62dbbae-487a-4751-9e7b-7b42494da8f9/GCF_009834925.2_ASM983492v2_genomic.fna.gz --refList GCF_009834925.2_ASM983492v2_genomic.fna/target_genomes.txt --output GCF_009834925.2_ASM983492v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:02,336] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:02,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:02,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:02,349] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:02,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:02,350] [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 guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	100.0	1388	1391	95	conclusive
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	92.7997	1023	1391	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	90.2473	899	1391	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	90.2306	903	1391	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	90.1614	937	1391	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	87.881	945	1391	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	87.8652	996	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:02,352] [INFO] DFAST Taxonomy check result was written to GCF_009834925.2_ASM983492v2_genomic.fna/tc_result.tsv
[2024-01-24 11:27:02,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:02,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:02,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference/checkm_data
[2024-01-24 11:27:02,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:02,393] [INFO] Task started: CheckM
[2024-01-24 11:27:02,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834925.2_ASM983492v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834925.2_ASM983492v2_genomic.fna/checkm_input GCF_009834925.2_ASM983492v2_genomic.fna/checkm_result
[2024-01-24 11:27:45,385] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:45,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:45,407] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:45,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:45,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834925.2_ASM983492v2_genomic.fna/markers.fasta)
[2024-01-24 11:27:45,409] [INFO] Task started: Blastn
[2024-01-24 11:27:45,409] [INFO] Running command: blastn -query GCF_009834925.2_ASM983492v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg922dd933-e88f-47e7-9a95-6be441b7c04e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834925.2_ASM983492v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:46,743] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:46,748] [INFO] Selected 7 target genomes.
[2024-01-24 11:27:46,748] [INFO] Target genome list was writen to GCF_009834925.2_ASM983492v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:46,758] [INFO] Task started: fastANI
[2024-01-24 11:27:46,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62dbbae-487a-4751-9e7b-7b42494da8f9/GCF_009834925.2_ASM983492v2_genomic.fna.gz --refList GCF_009834925.2_ASM983492v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009834925.2_ASM983492v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:53,409] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:53,422] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:53,423] [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_009834925.2	s__Eggerthella sp014287365	100.0	1389	1391	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	conclusive
GCF_900184265.1	s__Eggerthella timonensis	92.7875	1025	1391	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	90.1687	938	1391	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	87.8639	996	1391	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	85.2442	769	1391	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	84.8826	698	1391	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCA_018382595.1	s__Pauljensenia sp018382595	75.7842	52	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,424] [INFO] GTDB search result was written to GCF_009834925.2_ASM983492v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:53,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:53,428] [INFO] DFAST_QC result json was written to GCF_009834925.2_ASM983492v2_genomic.fna/dqc_result.json
[2024-01-24 11:27:53,428] [INFO] DFAST_QC completed!
[2024-01-24 11:27:53,428] [INFO] Total running time: 0h1m14s