[2024-01-24 12:21:44,648] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference
[2024-01-24 12:21:45,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,926] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg931bf9af-1813-44b8-a441-8e147e6de867/GCF_023923205.1_ASM2392320v1_genomic.fna.gz | prodigal -d GCF_023923205.1_ASM2392320v1_genomic.fna/cds.fna -a GCF_023923205.1_ASM2392320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:57,693] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:57,694] [INFO] Task started: HMMsearch
[2024-01-24 12:21:57,694] [INFO] Running command: hmmsearch --tblout GCF_023923205.1_ASM2392320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference/reference_markers.hmm GCF_023923205.1_ASM2392320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:58,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:58,050] [INFO] Found 6/6 markers.
[2024-01-24 12:21:58,104] [INFO] Query marker FASTA was written to GCF_023923205.1_ASM2392320v1_genomic.fna/markers.fasta
[2024-01-24 12:21:58,104] [INFO] Task started: Blastn
[2024-01-24 12:21:58,105] [INFO] Running command: blastn -query GCF_023923205.1_ASM2392320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference/reference_markers.fasta -out GCF_023923205.1_ASM2392320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:59,321] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:59,326] [INFO] Selected 20 target genomes.
[2024-01-24 12:21:59,327] [INFO] Target genome list was writen to GCF_023923205.1_ASM2392320v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:59,336] [INFO] Task started: fastANI
[2024-01-24 12:21:59,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg931bf9af-1813-44b8-a441-8e147e6de867/GCF_023923205.1_ASM2392320v1_genomic.fna.gz --refList GCF_023923205.1_ASM2392320v1_genomic.fna/target_genomes.txt --output GCF_023923205.1_ASM2392320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:15,299] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:15,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:15,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:15,319] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:15,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:15,320] [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
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	82.9133	790	1257	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	82.109	777	1257	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	81.6825	532	1257	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	80.0331	568	1257	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	79.8568	605	1257	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	79.5142	524	1257	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.4759	469	1257	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	79.4044	530	1257	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	79.3904	461	1257	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	79.157	461	1257	95	below_threshold
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	79.1543	429	1257	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	79.1011	475	1257	95	below_threshold
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	79.0508	461	1257	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	78.8873	451	1257	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	78.7526	435	1257	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	78.5563	460	1257	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.0012	305	1257	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	77.9243	318	1257	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	77.9187	335	1257	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_003149195.1	672460	672460	type	True	77.8448	231	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:15,322] [INFO] DFAST Taxonomy check result was written to GCF_023923205.1_ASM2392320v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:15,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:15,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:15,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference/checkm_data
[2024-01-24 12:22:15,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:15,368] [INFO] Task started: CheckM
[2024-01-24 12:22:15,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023923205.1_ASM2392320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023923205.1_ASM2392320v1_genomic.fna/checkm_input GCF_023923205.1_ASM2392320v1_genomic.fna/checkm_result
[2024-01-24 12:23:23,181] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:23,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,209] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:23,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:23,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023923205.1_ASM2392320v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:23,210] [INFO] Task started: Blastn
[2024-01-24 12:23:23,210] [INFO] Running command: blastn -query GCF_023923205.1_ASM2392320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf814ab3e-c4f8-4b94-857f-b7e4ebea1c8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_023923205.1_ASM2392320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,964] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,970] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:24,970] [INFO] Target genome list was writen to GCF_023923205.1_ASM2392320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:24,983] [INFO] Task started: fastANI
[2024-01-24 12:23:24,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg931bf9af-1813-44b8-a441-8e147e6de867/GCF_023923205.1_ASM2392320v1_genomic.fna.gz --refList GCF_023923205.1_ASM2392320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023923205.1_ASM2392320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:36,825] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,839] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:36,839] [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_007197575.1	s__Ornithinicoccus sp007197575	82.8683	790	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121625.1	s__Ornithinicoccus cavernae	82.1251	775	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	81.9657	649	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352835.1	s__Ornithinicoccus muralis	81.6788	533	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716185.1	s__Ornithinicoccus hortensis	79.873	607	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	79.6752	471	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	79.5023	530	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	79.3912	461	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685415.1	s__Serinicoccus hydrothermalis	79.1859	458	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602535.1	s__Ornithinicoccus_A halotolerans	79.1543	429	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	79.0726	484	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
GCF_004153545.1	s__Serinicoccus sediminis	78.7431	436	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	78.5742	458	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192725.1	s__Segeticoccus rhizosphaerae	78.3609	305	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Segeticoccus	95.0	99.13	99.13	0.90	0.90	2	-
GCF_003002895.1	s__Knoellia remsis	78.0201	304	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013135345.1	s__Yimella sp013135345	77.9994	293	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014190805.1	s__Flexivirga oryzae	77.8023	318	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,841] [INFO] GTDB search result was written to GCF_023923205.1_ASM2392320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:36,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:36,847] [INFO] DFAST_QC result json was written to GCF_023923205.1_ASM2392320v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:36,847] [INFO] DFAST_QC completed!
[2024-01-24 12:23:36,847] [INFO] Total running time: 0h1m52s