[2024-01-24 10:57:50,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference
[2024-01-24 10:57:52,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,642] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,642] [INFO] Running command: gunzip -c /var/lib/cwl/stga6616d56-b43c-4d29-a8c0-2a406419a9c4/GCF_030296655.1_ASM3029665v1_genomic.fna.gz | prodigal -d GCF_030296655.1_ASM3029665v1_genomic.fna/cds.fna -a GCF_030296655.1_ASM3029665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:02,895] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:02,896] [INFO] Task started: HMMsearch
[2024-01-24 10:58:02,896] [INFO] Running command: hmmsearch --tblout GCF_030296655.1_ASM3029665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference/reference_markers.hmm GCF_030296655.1_ASM3029665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:03,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:03,168] [INFO] Found 6/6 markers.
[2024-01-24 10:58:03,199] [INFO] Query marker FASTA was written to GCF_030296655.1_ASM3029665v1_genomic.fna/markers.fasta
[2024-01-24 10:58:03,200] [INFO] Task started: Blastn
[2024-01-24 10:58:03,200] [INFO] Running command: blastn -query GCF_030296655.1_ASM3029665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference/reference_markers.fasta -out GCF_030296655.1_ASM3029665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:04,460] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:04,464] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:04,464] [INFO] Target genome list was writen to GCF_030296655.1_ASM3029665v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:04,494] [INFO] Task started: fastANI
[2024-01-24 10:58:04,494] [INFO] Running command: fastANI --query /var/lib/cwl/stga6616d56-b43c-4d29-a8c0-2a406419a9c4/GCF_030296655.1_ASM3029665v1_genomic.fna.gz --refList GCF_030296655.1_ASM3029665v1_genomic.fna/target_genomes.txt --output GCF_030296655.1_ASM3029665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:21,420] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:21,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:21,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:21,438] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:21,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:21,439] [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=type strain: 39	GCA_910573815.1	999931	999931	type	True	98.2729	1143	1228	95	conclusive
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	98.2593	1158	1228	95	conclusive
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	81.2398	745	1228	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	80.4208	676	1228	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	79.5708	536	1228	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.4069	516	1228	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.275	464	1228	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.0717	530	1228	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	79.0058	471	1228	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.9803	461	1228	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.9181	536	1228	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	78.6802	444	1228	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	78.6101	444	1228	95	below_threshold
Demetria terragena	strain=DSM 11295	GCA_000376825.1	63959	63959	type	True	78.5535	393	1228	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.5308	503	1228	95	below_threshold
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	77.0786	341	1228	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	76.8705	325	1228	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.7485	525	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:21,440] [INFO] DFAST Taxonomy check result was written to GCF_030296655.1_ASM3029665v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:21,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:21,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:21,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference/checkm_data
[2024-01-24 10:58:21,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:21,487] [INFO] Task started: CheckM
[2024-01-24 10:58:21,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296655.1_ASM3029665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296655.1_ASM3029665v1_genomic.fna/checkm_input GCF_030296655.1_ASM3029665v1_genomic.fna/checkm_result
[2024-01-24 10:59:18,138] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:18,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:18,160] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:18,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:18,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296655.1_ASM3029665v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:18,161] [INFO] Task started: Blastn
[2024-01-24 10:59:18,162] [INFO] Running command: blastn -query GCF_030296655.1_ASM3029665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a7a2cd8-0f3f-40ce-bbad-0e073b74001c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296655.1_ASM3029665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,189] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,194] [INFO] Selected 19 target genomes.
[2024-01-24 10:59:20,194] [INFO] Target genome list was writen to GCF_030296655.1_ASM3029665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:20,224] [INFO] Task started: fastANI
[2024-01-24 10:59:20,224] [INFO] Running command: fastANI --query /var/lib/cwl/stga6616d56-b43c-4d29-a8c0-2a406419a9c4/GCF_030296655.1_ASM3029665v1_genomic.fna.gz --refList GCF_030296655.1_ASM3029665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296655.1_ASM3029665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:36,948] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:36,969] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:36,969] [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	98.2593	1158	1228	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	81.2249	748	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	80.4757	673	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	80.0976	536	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386865.1	s__Yimella indica	79.8956	566	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410455.1	s__Allobranchiibius huperziae	79.8377	512	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	97.04	97.04	0.91	0.91	2	-
GCF_900111375.1	s__Pedococcus cremeus	79.7571	537	1228	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	79.5625	540	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654605.1	s__Yimella sp014530045	79.522	434	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.79	97.58	0.96	0.92	3	-
GCF_002846495.1	s__Phycicoccus duodecadis	79.4313	493	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	79.4249	514	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426245.1	s__Pedococcus sp001426245	79.2686	502	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_014646815.1	s__Terrabacter tumescens	78.9965	529	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201035.1	s__Phycicoccus sp013201035	78.9455	554	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.9417	533	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_000376825.1	s__Demetria terragena	78.6073	393	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Demetria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153545.1	s__Serinicoccus sediminis	78.5787	448	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717165.1	s__JADKGA01 sp016717165	78.1798	374	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JADKGA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418575.1	s__Streptomyces_D griseoplanus	77.0715	342	1228	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 10:59:36,971] [INFO] GTDB search result was written to GCF_030296655.1_ASM3029665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:36,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:36,975] [INFO] DFAST_QC result json was written to GCF_030296655.1_ASM3029665v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:36,975] [INFO] DFAST_QC completed!
[2024-01-24 10:59:36,976] [INFO] Total running time: 0h1m47s