[2024-01-25 18:49:50,547] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:50,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:50,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference
[2024-01-25 18:49:51,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:51,790] [INFO] Task started: Prodigal
[2024-01-25 18:49:51,790] [INFO] Running command: gunzip -c /var/lib/cwl/stge49e1250-0956-4365-a870-6495eb525819/GCF_000971255.1_ASM97125v1_genomic.fna.gz | prodigal -d GCF_000971255.1_ASM97125v1_genomic.fna/cds.fna -a GCF_000971255.1_ASM97125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:59,500] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:59,501] [INFO] Task started: HMMsearch
[2024-01-25 18:49:59,501] [INFO] Running command: hmmsearch --tblout GCF_000971255.1_ASM97125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference/reference_markers.hmm GCF_000971255.1_ASM97125v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:59,717] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:59,718] [INFO] Found 6/6 markers.
[2024-01-25 18:49:59,750] [INFO] Query marker FASTA was written to GCF_000971255.1_ASM97125v1_genomic.fna/markers.fasta
[2024-01-25 18:49:59,750] [INFO] Task started: Blastn
[2024-01-25 18:49:59,750] [INFO] Running command: blastn -query GCF_000971255.1_ASM97125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference/reference_markers.fasta -out GCF_000971255.1_ASM97125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:01,169] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:01,173] [INFO] Selected 13 target genomes.
[2024-01-25 18:50:01,173] [INFO] Target genome list was writen to GCF_000971255.1_ASM97125v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:01,192] [INFO] Task started: fastANI
[2024-01-25 18:50:01,193] [INFO] Running command: fastANI --query /var/lib/cwl/stge49e1250-0956-4365-a870-6495eb525819/GCF_000971255.1_ASM97125v1_genomic.fna.gz --refList GCF_000971255.1_ASM97125v1_genomic.fna/target_genomes.txt --output GCF_000971255.1_ASM97125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:10,896] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:10,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:10,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:10,905] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:10,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:10,906] [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
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	100.0	1004	1004	95	conclusive
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	91.0957	863	1004	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	86.929	744	1004	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	86.552	748	1004	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	86.5422	771	1004	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	86.511	757	1004	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	86.4187	747	1004	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	85.8447	747	1004	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.2959	450	1004	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.1213	453	1004	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.4095	313	1004	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	77.33	327	1004	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.2907	196	1004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:10,907] [INFO] DFAST Taxonomy check result was written to GCF_000971255.1_ASM97125v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:10,908] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:10,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:10,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference/checkm_data
[2024-01-25 18:50:10,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:10,941] [INFO] Task started: CheckM
[2024-01-25 18:50:10,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000971255.1_ASM97125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000971255.1_ASM97125v1_genomic.fna/checkm_input GCF_000971255.1_ASM97125v1_genomic.fna/checkm_result
[2024-01-25 18:50:51,421] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:51,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:51,439] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:51,439] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:51,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000971255.1_ASM97125v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:51,440] [INFO] Task started: Blastn
[2024-01-25 18:50:51,440] [INFO] Running command: blastn -query GCF_000971255.1_ASM97125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89daedab-da7f-4a14-8822-4d326106712d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000971255.1_ASM97125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:53,908] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:53,911] [INFO] Selected 8 target genomes.
[2024-01-25 18:50:53,911] [INFO] Target genome list was writen to GCF_000971255.1_ASM97125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:53,919] [INFO] Task started: fastANI
[2024-01-25 18:50:53,919] [INFO] Running command: fastANI --query /var/lib/cwl/stge49e1250-0956-4365-a870-6495eb525819/GCF_000971255.1_ASM97125v1_genomic.fna.gz --refList GCF_000971255.1_ASM97125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000971255.1_ASM97125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:00,425] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:00,432] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:00,432] [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_000971255.1	s__Demequina rhizosphaerae	100.0	1004	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	conclusive
GCF_000971155.1	s__Demequina maris	91.1195	861	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	-
GCF_000971215.1	s__Demequina silvatica	86.8958	746	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759715.1	s__Demequina mangrovi	86.5384	750	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971135.1	s__Demequina phytophila	86.5268	772	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	86.4951	758	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971235.1	s__Demequina subtropica	85.7991	750	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971395.1	s__Demequina iriomotensis	85.4406	756	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:00,433] [INFO] GTDB search result was written to GCF_000971255.1_ASM97125v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:00,434] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:00,437] [INFO] DFAST_QC result json was written to GCF_000971255.1_ASM97125v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:00,437] [INFO] DFAST_QC completed!
[2024-01-25 18:51:00,437] [INFO] Total running time: 0h1m10s