[2024-01-24 12:15:04,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference
[2024-01-24 12:15:05,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,321] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg33fdfa0a-e2cb-4cf8-9363-8bc04b7ce900/GCF_001570845.1_ASM157084v1_genomic.fna.gz | prodigal -d GCF_001570845.1_ASM157084v1_genomic.fna/cds.fna -a GCF_001570845.1_ASM157084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:14,960] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:14,961] [INFO] Task started: HMMsearch
[2024-01-24 12:15:14,961] [INFO] Running command: hmmsearch --tblout GCF_001570845.1_ASM157084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference/reference_markers.hmm GCF_001570845.1_ASM157084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:15,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:15,221] [INFO] Found 6/6 markers.
[2024-01-24 12:15:15,264] [INFO] Query marker FASTA was written to GCF_001570845.1_ASM157084v1_genomic.fna/markers.fasta
[2024-01-24 12:15:15,265] [INFO] Task started: Blastn
[2024-01-24 12:15:15,265] [INFO] Running command: blastn -query GCF_001570845.1_ASM157084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference/reference_markers.fasta -out GCF_001570845.1_ASM157084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:16,436] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:16,439] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:16,440] [INFO] Target genome list was writen to GCF_001570845.1_ASM157084v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:16,446] [INFO] Task started: fastANI
[2024-01-24 12:15:16,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg33fdfa0a-e2cb-4cf8-9363-8bc04b7ce900/GCF_001570845.1_ASM157084v1_genomic.fna.gz --refList GCF_001570845.1_ASM157084v1_genomic.fna/target_genomes.txt --output GCF_001570845.1_ASM157084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:23,044] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:23,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:23,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:23,053] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:23,053] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:15:23,053] [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
Dietzia cinnamea	strain=NBRC 102147	GCA_001571065.1	321318	321318	type	True	98.1122	986	1099	95	inconclusive
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	95.4952	932	1099	95	inconclusive
Dietzia lutea	strain=YIM 80766	GCA_003096075.1	546160	546160	type	True	93.5025	958	1099	95	below_threshold
Dietzia lutea	strain=YIM 80766	GCA_009806405.1	546160	546160	type	True	92.5716	554	1099	95	below_threshold
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	86.291	916	1099	95	below_threshold
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	86.1946	613	1099	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	86.1532	910	1099	95	below_threshold
Dietzia aerolata	strain=Sj14aT	GCA_014144865.1	595984	595984	type	True	82.8156	620	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,055] [INFO] DFAST Taxonomy check result was written to GCF_001570845.1_ASM157084v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:23,056] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:23,056] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:23,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference/checkm_data
[2024-01-24 12:15:23,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:23,094] [INFO] Task started: CheckM
[2024-01-24 12:15:23,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001570845.1_ASM157084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001570845.1_ASM157084v1_genomic.fna/checkm_input GCF_001570845.1_ASM157084v1_genomic.fna/checkm_result
[2024-01-24 12:15:55,925] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:55,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:55,947] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:55,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:55,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001570845.1_ASM157084v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:55,948] [INFO] Task started: Blastn
[2024-01-24 12:15:55,948] [INFO] Running command: blastn -query GCF_001570845.1_ASM157084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf03cb46-8dfc-41df-9f0b-64a05cbb6bfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001570845.1_ASM157084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:57,586] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:57,590] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:57,591] [INFO] Target genome list was writen to GCF_001570845.1_ASM157084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:57,597] [INFO] Task started: fastANI
[2024-01-24 12:15:57,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg33fdfa0a-e2cb-4cf8-9363-8bc04b7ce900/GCF_001570845.1_ASM157084v1_genomic.fna.gz --refList GCF_001570845.1_ASM157084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001570845.1_ASM157084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:03,593] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:03,604] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:03,605] [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_001571065.1	s__Dietzia cinnamea	98.1122	986	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	97.27	96.55	0.88	0.84	8	conclusive
GCF_000186325.1	s__Dietzia cinnamea_A	94.9308	829	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	96.59	96.10	0.87	0.83	4	-
GCF_003096075.1	s__Dietzia lutea	93.5025	958	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014144855.1	s__Dietzia maris	86.2653	578	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	-
GCF_008369165.1	s__Dietzia sp008369165	83.8129	807	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012841845.1	s__Dietzia sp012841845	83.3222	464	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014144865.1	s__Dietzia aerolata	82.8192	620	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.62	97.62	0.76	0.76	2	-
GCA_019119635.1	s__Dietzia intestinipullorum	81.8609	680	1099	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:03,607] [INFO] GTDB search result was written to GCF_001570845.1_ASM157084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:03,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:03,610] [INFO] DFAST_QC result json was written to GCF_001570845.1_ASM157084v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:03,610] [INFO] DFAST_QC completed!
[2024-01-24 12:16:03,610] [INFO] Total running time: 0h0m60s