[2024-01-25 17:43:20,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:20,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:20,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference
[2024-01-25 17:43:21,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:21,763] [INFO] Task started: Prodigal
[2024-01-25 17:43:21,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg96b74cc3-2c2b-4dfd-977a-097680f5bcdd/GCF_003710105.1_ASM371010v1_genomic.fna.gz | prodigal -d GCF_003710105.1_ASM371010v1_genomic.fna/cds.fna -a GCF_003710105.1_ASM371010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:30,043] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:30,044] [INFO] Task started: HMMsearch
[2024-01-25 17:43:30,044] [INFO] Running command: hmmsearch --tblout GCF_003710105.1_ASM371010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference/reference_markers.hmm GCF_003710105.1_ASM371010v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:30,268] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:30,269] [INFO] Found 6/6 markers.
[2024-01-25 17:43:30,298] [INFO] Query marker FASTA was written to GCF_003710105.1_ASM371010v1_genomic.fna/markers.fasta
[2024-01-25 17:43:30,299] [INFO] Task started: Blastn
[2024-01-25 17:43:30,299] [INFO] Running command: blastn -query GCF_003710105.1_ASM371010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference/reference_markers.fasta -out GCF_003710105.1_ASM371010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:31,588] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:31,591] [INFO] Selected 14 target genomes.
[2024-01-25 17:43:31,591] [INFO] Target genome list was writen to GCF_003710105.1_ASM371010v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:31,600] [INFO] Task started: fastANI
[2024-01-25 17:43:31,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b74cc3-2c2b-4dfd-977a-097680f5bcdd/GCF_003710105.1_ASM371010v1_genomic.fna.gz --refList GCF_003710105.1_ASM371010v1_genomic.fna/target_genomes.txt --output GCF_003710105.1_ASM371010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:44,774] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:44,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:44,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:44,784] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:44,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:44,784] [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
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	100.0	1144	1144	95	conclusive
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	81.4342	661	1144	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	81.2108	634	1144	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	79.8913	570	1144	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	79.8222	559	1144	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	79.658	564	1144	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	79.3999	542	1144	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	79.3176	515	1144	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	79.2553	518	1144	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.3548	497	1144	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.9679	524	1144	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.9242	523	1144	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.8768	447	1144	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	77.3471	497	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:44,785] [INFO] DFAST Taxonomy check result was written to GCF_003710105.1_ASM371010v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:44,786] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:44,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:44,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference/checkm_data
[2024-01-25 17:43:44,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:44,826] [INFO] Task started: CheckM
[2024-01-25 17:43:44,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710105.1_ASM371010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710105.1_ASM371010v1_genomic.fna/checkm_input GCF_003710105.1_ASM371010v1_genomic.fna/checkm_result
[2024-01-25 17:44:40,171] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:40,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:40,191] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:40,191] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:40,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710105.1_ASM371010v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:40,192] [INFO] Task started: Blastn
[2024-01-25 17:44:40,192] [INFO] Running command: blastn -query GCF_003710105.1_ASM371010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8352d255-7898-4016-ac8b-e30c8adf5d9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710105.1_ASM371010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:42,453] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:42,455] [INFO] Selected 8 target genomes.
[2024-01-25 17:44:42,456] [INFO] Target genome list was writen to GCF_003710105.1_ASM371010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:42,476] [INFO] Task started: fastANI
[2024-01-25 17:44:42,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b74cc3-2c2b-4dfd-977a-097680f5bcdd/GCF_003710105.1_ASM371010v1_genomic.fna.gz --refList GCF_003710105.1_ASM371010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710105.1_ASM371010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:49,888] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:49,894] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:49,894] [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_003710105.1	s__Georgenia_A faecalis	100.0	1144	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia_A	95.0	99.15	99.15	0.96	0.96	2	conclusive
GCF_006349365.1	s__Oceanitalea sp006349365	81.4141	664	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	99.20	99.20	0.95	0.95	2	-
GCA_014837105.1	s__Oceanitalea sp014837105	81.1928	636	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193135.1	s__Oceanitalea satyanarayanai	80.9961	635	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	80.8777	652	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003814705.1	s__Georgenia muralis	79.7836	562	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991205.1	s__Georgenia sp003991205	79.5618	555	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352065.1	s__Georgenia sp006352065	79.299	523	1144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:49,895] [INFO] GTDB search result was written to GCF_003710105.1_ASM371010v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:49,896] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:49,899] [INFO] DFAST_QC result json was written to GCF_003710105.1_ASM371010v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:49,899] [INFO] DFAST_QC completed!
[2024-01-25 17:44:49,899] [INFO] Total running time: 0h1m29s