[2024-01-24 14:21:50,862] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,867] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference
[2024-01-24 14:21:52,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,289] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,289] [INFO] Running command: gunzip -c /var/lib/cwl/stgd155ebe6-d878-41bf-8e17-5472a9025eb2/GCF_006716095.1_ASM671609v1_genomic.fna.gz | prodigal -d GCF_006716095.1_ASM671609v1_genomic.fna/cds.fna -a GCF_006716095.1_ASM671609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:03,301] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:03,302] [INFO] Task started: HMMsearch
[2024-01-24 14:22:03,302] [INFO] Running command: hmmsearch --tblout GCF_006716095.1_ASM671609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference/reference_markers.hmm GCF_006716095.1_ASM671609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:03,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:03,615] [INFO] Found 6/6 markers.
[2024-01-24 14:22:03,649] [INFO] Query marker FASTA was written to GCF_006716095.1_ASM671609v1_genomic.fna/markers.fasta
[2024-01-24 14:22:03,650] [INFO] Task started: Blastn
[2024-01-24 14:22:03,650] [INFO] Running command: blastn -query GCF_006716095.1_ASM671609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference/reference_markers.fasta -out GCF_006716095.1_ASM671609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:05,063] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:05,066] [INFO] Selected 20 target genomes.
[2024-01-24 14:22:05,067] [INFO] Target genome list was writen to GCF_006716095.1_ASM671609v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:05,093] [INFO] Task started: fastANI
[2024-01-24 14:22:05,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgd155ebe6-d878-41bf-8e17-5472a9025eb2/GCF_006716095.1_ASM671609v1_genomic.fna.gz --refList GCF_006716095.1_ASM671609v1_genomic.fna/target_genomes.txt --output GCF_006716095.1_ASM671609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:25,149] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:25,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:25,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:25,176] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:25,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:25,176] [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
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	100.0	1212	1214	95	conclusive
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	99.9959	1196	1214	95	conclusive
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	81.4233	723	1214	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	80.3087	631	1214	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	80.2539	682	1214	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	79.5255	538	1214	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.2803	524	1214	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	79.1984	508	1214	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.0876	464	1214	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	79.0794	463	1214	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.8548	540	1214	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	78.8311	422	1214	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	78.7896	553	1214	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.7842	478	1214	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.6413	496	1214	95	below_threshold
Cellulomonas citrea	strain=Ao-9	GCA_009829685.1	1909423	1909423	type	True	77.1803	314	1214	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	77.0101	344	1214	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	76.8588	316	1214	95	below_threshold
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	76.8379	357	1214	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.7273	528	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:25,178] [INFO] DFAST Taxonomy check result was written to GCF_006716095.1_ASM671609v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:25,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:25,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:25,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference/checkm_data
[2024-01-24 14:22:25,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:25,217] [INFO] Task started: CheckM
[2024-01-24 14:22:25,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716095.1_ASM671609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716095.1_ASM671609v1_genomic.fna/checkm_input GCF_006716095.1_ASM671609v1_genomic.fna/checkm_result
[2024-01-24 14:23:19,072] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:19,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:19,095] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:19,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:19,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716095.1_ASM671609v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:19,096] [INFO] Task started: Blastn
[2024-01-24 14:23:19,097] [INFO] Running command: blastn -query GCF_006716095.1_ASM671609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e05abc-20d8-46da-a163-794e8b411708/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716095.1_ASM671609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:21,318] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:21,323] [INFO] Selected 21 target genomes.
[2024-01-24 14:23:21,323] [INFO] Target genome list was writen to GCF_006716095.1_ASM671609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:21,341] [INFO] Task started: fastANI
[2024-01-24 14:23:21,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgd155ebe6-d878-41bf-8e17-5472a9025eb2/GCF_006716095.1_ASM671609v1_genomic.fna.gz --refList GCF_006716095.1_ASM671609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716095.1_ASM671609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:42,637] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:42,656] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:42,657] [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_006716095.1	s__Barrientosiimonas humi	100.0	1212	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_001247745.1	s__Luteipulveratus halotolerans	81.4216	723	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013002715.1	s__Flexivirga aerilata	80.3004	632	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	80.2486	683	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386865.1	s__Yimella indica	80.06	559	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.92	545	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	79.6791	535	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_014190805.1	s__Flexivirga oryzae	79.585	535	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410455.1	s__Allobranchiibius huperziae	79.5452	538	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	97.04	97.04	0.91	0.91	2	-
GCF_017654605.1	s__Yimella sp014530045	79.465	450	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.79	97.58	0.96	0.92	3	-
GCF_900104525.1	s__Pedococcus dokdonensis	79.2722	525	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715095.1	s__Yimella lutea	79.1876	480	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.40	98.40	0.90	0.90	2	-
GCF_014640635.1	s__Flexivirga endophytica	79.1393	513	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715875.1	s__Terrabacter sp006715875	79.058	537	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.8471	541	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_013201035.1	s__Phycicoccus sp013201035	78.845	549	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383675.1	s__Terrabacter sp000383675	78.7715	515	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716915.1	s__Terrabacter sp006716915	78.7035	514	1214	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	78.6053	492	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153545.1	s__Serinicoccus sediminis	78.5471	450	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418575.1	s__Streptomyces_D griseoplanus	76.8633	353	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:42,658] [INFO] GTDB search result was written to GCF_006716095.1_ASM671609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:42,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:42,663] [INFO] DFAST_QC result json was written to GCF_006716095.1_ASM671609v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:42,663] [INFO] DFAST_QC completed!
[2024-01-24 14:23:42,663] [INFO] Total running time: 0h1m52s