[2024-01-24 15:10:20,278] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,280] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,280] [INFO] DQC Reference Directory: /var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference
[2024-01-24 15:10:23,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:23,847] [INFO] Task started: Prodigal
[2024-01-24 15:10:23,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg50e86b33-afe7-4754-b0de-fc9444c81716/GCF_009193135.1_ASM919313v1_genomic.fna.gz | prodigal -d GCF_009193135.1_ASM919313v1_genomic.fna/cds.fna -a GCF_009193135.1_ASM919313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:33,752] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:33,752] [INFO] Task started: HMMsearch
[2024-01-24 15:10:33,752] [INFO] Running command: hmmsearch --tblout GCF_009193135.1_ASM919313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference/reference_markers.hmm GCF_009193135.1_ASM919313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:33,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:33,978] [INFO] Found 6/6 markers.
[2024-01-24 15:10:34,008] [INFO] Query marker FASTA was written to GCF_009193135.1_ASM919313v1_genomic.fna/markers.fasta
[2024-01-24 15:10:34,008] [INFO] Task started: Blastn
[2024-01-24 15:10:34,009] [INFO] Running command: blastn -query GCF_009193135.1_ASM919313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference/reference_markers.fasta -out GCF_009193135.1_ASM919313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:35,325] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:35,328] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:35,329] [INFO] Target genome list was writen to GCF_009193135.1_ASM919313v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:35,335] [INFO] Task started: fastANI
[2024-01-24 15:10:35,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg50e86b33-afe7-4754-b0de-fc9444c81716/GCF_009193135.1_ASM919313v1_genomic.fna.gz --refList GCF_009193135.1_ASM919313v1_genomic.fna/target_genomes.txt --output GCF_009193135.1_ASM919313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:47,121] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:47,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:47,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:47,132] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:10:47,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:10:47,133] [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
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	91.2943	972	1135	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	85.0743	841	1135	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	80.9369	640	1135	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	79.7897	589	1135	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	79.7133	567	1135	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	79.6995	569	1135	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	79.4934	570	1135	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	79.4527	566	1135	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	79.4109	538	1135	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	79.2923	517	1135	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.0354	518	1135	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.5538	447	1135	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.4915	410	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:47,135] [INFO] DFAST Taxonomy check result was written to GCF_009193135.1_ASM919313v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:47,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:47,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:47,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference/checkm_data
[2024-01-24 15:10:47,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:47,170] [INFO] Task started: CheckM
[2024-01-24 15:10:47,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193135.1_ASM919313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193135.1_ASM919313v1_genomic.fna/checkm_input GCF_009193135.1_ASM919313v1_genomic.fna/checkm_result
[2024-01-24 15:11:35,559] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:35,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:35,578] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:35,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:35,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193135.1_ASM919313v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:35,578] [INFO] Task started: Blastn
[2024-01-24 15:11:35,578] [INFO] Running command: blastn -query GCF_009193135.1_ASM919313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge39beccd-d74e-4ad6-9c41-58c047cc9b70/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193135.1_ASM919313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:37,865] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:37,868] [INFO] Selected 6 target genomes.
[2024-01-24 15:11:37,868] [INFO] Target genome list was writen to GCF_009193135.1_ASM919313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:37,873] [INFO] Task started: fastANI
[2024-01-24 15:11:37,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg50e86b33-afe7-4754-b0de-fc9444c81716/GCF_009193135.1_ASM919313v1_genomic.fna.gz --refList GCF_009193135.1_ASM919313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009193135.1_ASM919313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:44,486] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:44,492] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:44,492] [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_009193135.1	s__Oceanitalea satyanarayanai	100.0	1132	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014837105.1	s__Oceanitalea sp014837105	91.3394	969	1135	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	91.3315	978	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006349365.1	s__Oceanitalea sp006349365	85.0522	843	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	99.20	99.20	0.95	0.95	2	-
GCF_003710105.1	s__Georgenia_A faecalis	80.9864	636	1135	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_009193175.1	s__Georgenia ruanii	79.7369	565	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:44,494] [INFO] GTDB search result was written to GCF_009193135.1_ASM919313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:44,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:44,499] [INFO] DFAST_QC result json was written to GCF_009193135.1_ASM919313v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:44,499] [INFO] DFAST_QC completed!
[2024-01-24 15:11:44,500] [INFO] Total running time: 0h1m24s