[2024-01-24 13:49:33,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference
[2024-01-24 13:49:34,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,433] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg80eb6268-ceb0-4288-a378-568fcabe3ea9/GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/cds.fna -a GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,974] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,975] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,975] [INFO] Running command: hmmsearch --tblout GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference/reference_markers.hmm GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,233] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,265] [INFO] Query marker FASTA was written to GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:43,266] [INFO] Task started: Blastn
[2024-01-24 13:49:43,266] [INFO] Running command: blastn -query GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference/reference_markers.fasta -out GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,943] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:43,943] [INFO] Target genome list was writen to GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,955] [INFO] Task started: fastANI
[2024-01-24 13:49:43,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg80eb6268-ceb0-4288-a378-568fcabe3ea9/GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna.gz --refList GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:53,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:53,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:53,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:53,168] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:53,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:53,169] [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
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	100.0	1130	1130	95	conclusive
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	80.3533	592	1130	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	77.9395	399	1130	95	below_threshold
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	77.7674	337	1130	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.2823	249	1130	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	75.4305	61	1130	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	75.1016	56	1130	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	75.0239	58	1130	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	74.9891	84	1130	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	74.819	102	1130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:53,171] [INFO] DFAST Taxonomy check result was written to GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:53,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:53,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:53,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference/checkm_data
[2024-01-24 13:49:53,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:53,215] [INFO] Task started: CheckM
[2024-01-24 13:49:53,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/checkm_input GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:22,579] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:22,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,601] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:22,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:22,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:22,603] [INFO] Task started: Blastn
[2024-01-24 13:50:22,603] [INFO] Running command: blastn -query GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5f9414-b385-4df1-bdc4-ccf41a0b30d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:23,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:23,589] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:23,589] [INFO] Target genome list was writen to GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:23,608] [INFO] Task started: fastANI
[2024-01-24 13:50:23,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg80eb6268-ceb0-4288-a378-568fcabe3ea9/GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna.gz --refList GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:34,532] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:34,551] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:34,551] [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_900175965.1	s__Rubrobacter radiotolerans	100.0	1130	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_003568865.1	s__Rubrobacter indicoceani	80.3633	591	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563715.1	s__SIRX01 sp004563715	78.1986	339	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011492965.1	s__SCSIO-52915 sp011492965	77.9386	399	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806105.1	s__SCSIO-52915 sp902806105	77.8823	295	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806085.1	s__SCSIO-52909 sp902806085	77.802	328	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781725.1	s__SCSIO-52909 sp016781725	77.7812	214	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCF_011492945.1	s__SCSIO-52909 sp011492945	77.7674	337	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812425.1	s__SCSIO-52909 sp902812425	77.6013	231	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007164525.1	s__Rubrobacter_B xylanophilus_A	77.586	310	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337705.1	s__Rubrobacter_C taiwanensis	77.4911	235	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697825.1	s__JACCWD01 sp013697825	77.3092	254	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACCWD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806095.1	s__SCSIO-52909 sp902806095	77.1866	204	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815485.1	s__JACDGB01 sp013815485	77.0837	135	1130	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACDGB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352065.1	s__Georgenia sp006352065	75.4305	61	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,553] [INFO] GTDB search result was written to GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:34,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:34,557] [INFO] DFAST_QC result json was written to GCF_900175965.1_IMG-taxon_2505679031_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:34,558] [INFO] DFAST_QC completed!
[2024-01-24 13:50:34,558] [INFO] Total running time: 0h1m2s