[2024-01-25 19:44:20,909] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:20,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:20,910] [INFO] DQC Reference Directory: /var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference
[2024-01-25 19:44:22,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:22,036] [INFO] Task started: Prodigal
[2024-01-25 19:44:22,036] [INFO] Running command: gunzip -c /var/lib/cwl/stg023b7d89-3d1c-44d9-a459-c38764f8328e/GCF_003814705.1_ASM381470v1_genomic.fna.gz | prodigal -d GCF_003814705.1_ASM381470v1_genomic.fna/cds.fna -a GCF_003814705.1_ASM381470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:32,266] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:32,267] [INFO] Task started: HMMsearch
[2024-01-25 19:44:32,267] [INFO] Running command: hmmsearch --tblout GCF_003814705.1_ASM381470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference/reference_markers.hmm GCF_003814705.1_ASM381470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:32,505] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:32,506] [INFO] Found 6/6 markers.
[2024-01-25 19:44:32,540] [INFO] Query marker FASTA was written to GCF_003814705.1_ASM381470v1_genomic.fna/markers.fasta
[2024-01-25 19:44:32,540] [INFO] Task started: Blastn
[2024-01-25 19:44:32,540] [INFO] Running command: blastn -query GCF_003814705.1_ASM381470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference/reference_markers.fasta -out GCF_003814705.1_ASM381470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:33,770] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:33,773] [INFO] Selected 12 target genomes.
[2024-01-25 19:44:33,773] [INFO] Target genome list was writen to GCF_003814705.1_ASM381470v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:33,780] [INFO] Task started: fastANI
[2024-01-25 19:44:33,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg023b7d89-3d1c-44d9-a459-c38764f8328e/GCF_003814705.1_ASM381470v1_genomic.fna.gz --refList GCF_003814705.1_ASM381470v1_genomic.fna/target_genomes.txt --output GCF_003814705.1_ASM381470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:45,324] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:45,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:45,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:45,333] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:45,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:45,333] [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 muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	100.0	1381	1381	95	conclusive
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	81.6465	670	1381	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	81.5218	741	1381	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	81.3058	725	1381	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	81.2376	711	1381	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	81.228	655	1381	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	81.2045	705	1381	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	81.0363	678	1381	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	79.8424	566	1381	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	79.7823	581	1381	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.7503	507	1381	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.667	438	1381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:45,334] [INFO] DFAST Taxonomy check result was written to GCF_003814705.1_ASM381470v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:45,335] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:45,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:45,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference/checkm_data
[2024-01-25 19:44:45,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:45,375] [INFO] Task started: CheckM
[2024-01-25 19:44:45,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003814705.1_ASM381470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003814705.1_ASM381470v1_genomic.fna/checkm_input GCF_003814705.1_ASM381470v1_genomic.fna/checkm_result
[2024-01-25 19:45:56,849] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:56,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:56,867] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:56,867] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:56,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003814705.1_ASM381470v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:56,868] [INFO] Task started: Blastn
[2024-01-25 19:45:56,868] [INFO] Running command: blastn -query GCF_003814705.1_ASM381470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4abb739-66dc-4f70-ab6d-da48801cbd0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003814705.1_ASM381470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:58,810] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:58,813] [INFO] Selected 10 target genomes.
[2024-01-25 19:45:58,813] [INFO] Target genome list was writen to GCF_003814705.1_ASM381470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:58,820] [INFO] Task started: fastANI
[2024-01-25 19:45:58,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg023b7d89-3d1c-44d9-a459-c38764f8328e/GCF_003814705.1_ASM381470v1_genomic.fna.gz --refList GCF_003814705.1_ASM381470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003814705.1_ASM381470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:09,162] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:09,169] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:09,170] [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_003814705.1	s__Georgenia muralis	100.0	1379	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009193185.1	s__Georgenia thermotolerans	81.5072	742	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009193175.1	s__Georgenia ruanii	81.3234	722	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193155.1	s__Georgenia subflava	81.2327	702	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002563695.1	s__Georgenia soli	81.2189	709	1381	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	81.0274	679	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_003991205.1	s__Georgenia sp003991205	81.0244	685	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014837105.1	s__Oceanitalea sp014837105	79.7823	581	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710105.1	s__Georgenia_A faecalis	79.6747	574	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia_A	95.0	99.15	99.15	0.96	0.96	2	-
GCF_902703175.1	s__Occultella aeris	77.6117	460	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:09,171] [INFO] GTDB search result was written to GCF_003814705.1_ASM381470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:09,171] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:09,174] [INFO] DFAST_QC result json was written to GCF_003814705.1_ASM381470v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:09,174] [INFO] DFAST_QC completed!
[2024-01-25 19:46:09,174] [INFO] Total running time: 0h1m48s