[2024-01-24 13:19:25,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference
[2024-01-24 13:19:26,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:26,812] [INFO] Task started: Prodigal
[2024-01-24 13:19:26,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bf71429-b4d2-4bfe-b32b-dfc025339f11/GCF_009299305.1_ASM929930v1_genomic.fna.gz | prodigal -d GCF_009299305.1_ASM929930v1_genomic.fna/cds.fna -a GCF_009299305.1_ASM929930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:38,268] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:38,269] [INFO] Task started: HMMsearch
[2024-01-24 13:19:38,269] [INFO] Running command: hmmsearch --tblout GCF_009299305.1_ASM929930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference/reference_markers.hmm GCF_009299305.1_ASM929930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:38,507] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:38,508] [INFO] Found 6/6 markers.
[2024-01-24 13:19:38,551] [INFO] Query marker FASTA was written to GCF_009299305.1_ASM929930v1_genomic.fna/markers.fasta
[2024-01-24 13:19:38,552] [INFO] Task started: Blastn
[2024-01-24 13:19:38,552] [INFO] Running command: blastn -query GCF_009299305.1_ASM929930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference/reference_markers.fasta -out GCF_009299305.1_ASM929930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:39,780] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:39,784] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:39,784] [INFO] Target genome list was writen to GCF_009299305.1_ASM929930v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:39,790] [INFO] Task started: fastANI
[2024-01-24 13:19:39,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf71429-b4d2-4bfe-b32b-dfc025339f11/GCF_009299305.1_ASM929930v1_genomic.fna.gz --refList GCF_009299305.1_ASM929930v1_genomic.fna/target_genomes.txt --output GCF_009299305.1_ASM929930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:51,936] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:51,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:51,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:51,947] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:51,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:51,948] [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 thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	100.0	1342	1355	95	conclusive
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	99.9882	1352	1355	95	conclusive
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	91.7635	1043	1355	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	83.2488	823	1355	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	81.8837	752	1355	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	81.5122	664	1355	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	81.4039	686	1355	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	81.3954	668	1355	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	79.6601	560	1355	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.8316	461	1355	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.8305	440	1355	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.7422	440	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:51,949] [INFO] DFAST Taxonomy check result was written to GCF_009299305.1_ASM929930v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:51,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:51,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:51,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference/checkm_data
[2024-01-24 13:19:51,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:51,992] [INFO] Task started: CheckM
[2024-01-24 13:19:51,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009299305.1_ASM929930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009299305.1_ASM929930v1_genomic.fna/checkm_input GCF_009299305.1_ASM929930v1_genomic.fna/checkm_result
[2024-01-24 13:20:45,636] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:45,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:45,655] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:45,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:45,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009299305.1_ASM929930v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:45,656] [INFO] Task started: Blastn
[2024-01-24 13:20:45,656] [INFO] Running command: blastn -query GCF_009299305.1_ASM929930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6fd413-98c2-4e0a-b760-d6a239e44145/dqc_reference/reference_markers_gtdb.fasta -out GCF_009299305.1_ASM929930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:47,616] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:47,619] [INFO] Selected 11 target genomes.
[2024-01-24 13:20:47,619] [INFO] Target genome list was writen to GCF_009299305.1_ASM929930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:47,641] [INFO] Task started: fastANI
[2024-01-24 13:20:47,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf71429-b4d2-4bfe-b32b-dfc025339f11/GCF_009299305.1_ASM929930v1_genomic.fna.gz --refList GCF_009299305.1_ASM929930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009299305.1_ASM929930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:58,995] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:59,004] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:59,005] [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_009193185.1	s__Georgenia thermotolerans	99.9882	1352	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_009193175.1	s__Georgenia ruanii	91.7142	1046	1355	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	83.2479	823	1355	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	82.4328	811	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563695.1	s__Georgenia soli	81.8321	758	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814705.1	s__Georgenia muralis	81.5282	662	1355	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	81.3579	692	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007991755.1	s__Cellulomonas aerilata	78.0915	477	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902703175.1	s__Occultella aeris	77.815	442	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009660225.1	s__HY158 sp009660225	77.6914	364	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__HY158	95.0	98.70	98.70	0.90	0.90	2	-
GCF_001424195.1	s__Cellulomonas sp001424195	77.5693	452	1355	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:59,006] [INFO] GTDB search result was written to GCF_009299305.1_ASM929930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:59,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:59,010] [INFO] DFAST_QC result json was written to GCF_009299305.1_ASM929930v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:59,010] [INFO] DFAST_QC completed!
[2024-01-24 13:20:59,010] [INFO] Total running time: 0h1m33s