[2024-01-25 20:06:50,993] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:50,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:50,995] [INFO] DQC Reference Directory: /var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference
[2024-01-25 20:06:52,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:52,118] [INFO] Task started: Prodigal
[2024-01-25 20:06:52,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg974abaac-e3c0-47ab-9514-9fcf4a3740ce/GCF_000184685.1_ASM18468v1_genomic.fna.gz | prodigal -d GCF_000184685.1_ASM18468v1_genomic.fna/cds.fna -a GCF_000184685.1_ASM18468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:02,376] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:02,377] [INFO] Task started: HMMsearch
[2024-01-25 20:07:02,377] [INFO] Running command: hmmsearch --tblout GCF_000184685.1_ASM18468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference/reference_markers.hmm GCF_000184685.1_ASM18468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:02,616] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:02,617] [INFO] Found 6/6 markers.
[2024-01-25 20:07:02,650] [INFO] Query marker FASTA was written to GCF_000184685.1_ASM18468v1_genomic.fna/markers.fasta
[2024-01-25 20:07:02,650] [INFO] Task started: Blastn
[2024-01-25 20:07:02,650] [INFO] Running command: blastn -query GCF_000184685.1_ASM18468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference/reference_markers.fasta -out GCF_000184685.1_ASM18468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:03,801] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:03,803] [INFO] Selected 21 target genomes.
[2024-01-25 20:07:03,804] [INFO] Target genome list was writen to GCF_000184685.1_ASM18468v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:03,819] [INFO] Task started: fastANI
[2024-01-25 20:07:03,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg974abaac-e3c0-47ab-9514-9fcf4a3740ce/GCF_000184685.1_ASM18468v1_genomic.fna.gz --refList GCF_000184685.1_ASM18468v1_genomic.fna/target_genomes.txt --output GCF_000184685.1_ASM18468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:19,003] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:19,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:19,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:19,016] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:19,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:19,017] [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
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	100.0	1340	1341	95	conclusive
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	80.8326	604	1341	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.4036	547	1341	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	79.3661	498	1341	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	79.3201	512	1341	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.202	407	1341	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	79.1798	470	1341	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.1501	537	1341	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	79.0224	437	1341	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	78.9582	501	1341	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	78.6725	436	1341	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	78.6722	394	1341	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.4631	416	1341	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.3106	418	1341	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.2844	413	1341	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.2531	371	1341	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	77.9326	334	1341	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.9089	331	1341	95	below_threshold
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	77.7265	319	1341	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	77.1664	296	1341	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	77.0747	277	1341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:19,018] [INFO] DFAST Taxonomy check result was written to GCF_000184685.1_ASM18468v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:19,018] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:19,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:19,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference/checkm_data
[2024-01-25 20:07:19,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:19,060] [INFO] Task started: CheckM
[2024-01-25 20:07:19,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000184685.1_ASM18468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000184685.1_ASM18468v1_genomic.fna/checkm_input GCF_000184685.1_ASM18468v1_genomic.fna/checkm_result
[2024-01-25 20:08:34,164] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:34,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:34,179] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:34,180] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:34,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000184685.1_ASM18468v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:34,181] [INFO] Task started: Blastn
[2024-01-25 20:08:34,181] [INFO] Running command: blastn -query GCF_000184685.1_ASM18468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefe4429d-51ff-4a63-8e22-98b427f2697d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000184685.1_ASM18468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:36,012] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:36,015] [INFO] Selected 14 target genomes.
[2024-01-25 20:08:36,015] [INFO] Target genome list was writen to GCF_000184685.1_ASM18468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:36,048] [INFO] Task started: fastANI
[2024-01-25 20:08:36,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg974abaac-e3c0-47ab-9514-9fcf4a3740ce/GCF_000184685.1_ASM18468v1_genomic.fna.gz --refList GCF_000184685.1_ASM18468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000184685.1_ASM18468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:49,918] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:49,927] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:49,927] [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_000184685.1	s__Intrasporangium calvum	100.0	1340	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Intrasporangium	95.0	99.10	99.10	0.92	0.92	2	conclusive
GCF_000576595.1	s__Humihabitans oryzae	81.5559	732	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991735.1	s__Terrabacter aerolatus	81.4797	755	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646815.1	s__Terrabacter tumescens	81.4567	772	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000955875.1	s__Terrabacter sp000955875	81.4531	785	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429185.1	s__Terrabacter sp001429185	81.3966	777	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
GCF_006715875.1	s__Terrabacter sp006715875	81.3712	733	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383675.1	s__Terrabacter sp000383675	81.3285	771	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	81.2155	657	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716675.1	s__Humibacillus xanthopallidus	81.2103	759	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716915.1	s__Terrabacter sp006716915	81.0984	760	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014518425.1	s__Terrabacter sp014518425	81.0577	773	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576575.1	s__Intrasporangium_A chromatireducens	80.8262	605	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Intrasporangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758225.1	s__Terracoccus sp001758225	79.5405	659	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:49,930] [INFO] GTDB search result was written to GCF_000184685.1_ASM18468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:49,931] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:49,935] [INFO] DFAST_QC result json was written to GCF_000184685.1_ASM18468v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:49,935] [INFO] DFAST_QC completed!
[2024-01-25 20:08:49,935] [INFO] Total running time: 0h1m59s