[2023-06-26 23:52:21,284] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:52:21,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:52:21,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference
[2023-06-26 23:52:22,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:52:22,511] [INFO] Task started: Prodigal
[2023-06-26 23:52:22,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg1648db04-a2b0-4775-8461-3bb0d3c618d9/GCA_002404345.1_ASM240434v1_genomic.fna.gz | prodigal -d GCA_002404345.1_ASM240434v1_genomic.fna/cds.fna -a GCA_002404345.1_ASM240434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:52:32,851] [INFO] Task succeeded: Prodigal
[2023-06-26 23:52:32,852] [INFO] Task started: HMMsearch
[2023-06-26 23:52:32,852] [INFO] Running command: hmmsearch --tblout GCA_002404345.1_ASM240434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference/reference_markers.hmm GCA_002404345.1_ASM240434v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:52:33,108] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:52:33,110] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1648db04-a2b0-4775-8461-3bb0d3c618d9/GCA_002404345.1_ASM240434v1_genomic.fna.gz]
[2023-06-26 23:52:33,317] [INFO] Query marker FASTA was written to GCA_002404345.1_ASM240434v1_genomic.fna/markers.fasta
[2023-06-26 23:52:33,318] [INFO] Task started: Blastn
[2023-06-26 23:52:33,318] [INFO] Running command: blastn -query GCA_002404345.1_ASM240434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference/reference_markers.fasta -out GCA_002404345.1_ASM240434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:52:34,065] [INFO] Task succeeded: Blastn
[2023-06-26 23:52:34,084] [INFO] Selected 28 target genomes.
[2023-06-26 23:52:34,085] [INFO] Target genome list was writen to GCA_002404345.1_ASM240434v1_genomic.fna/target_genomes.txt
[2023-06-26 23:52:34,096] [INFO] Task started: fastANI
[2023-06-26 23:52:34,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg1648db04-a2b0-4775-8461-3bb0d3c618d9/GCA_002404345.1_ASM240434v1_genomic.fna.gz --refList GCA_002404345.1_ASM240434v1_genomic.fna/target_genomes.txt --output GCA_002404345.1_ASM240434v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:52:52,572] [INFO] Task succeeded: fastANI
[2023-06-26 23:52:52,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:52:52,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:52:52,595] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:52:52,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:52:52,596] [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
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	78.2651	337	1118	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.171	373	1118	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	77.7941	273	1118	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	77.7504	276	1118	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	77.71	272	1118	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	77.69	271	1118	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	77.6601	266	1118	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	77.6585	276	1118	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	77.5858	279	1118	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	77.579	257	1118	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	77.5364	253	1118	95	below_threshold
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	77.4912	247	1118	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	77.419	231	1118	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.3611	230	1118	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	77.3567	227	1118	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	77.3209	237	1118	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	77.3041	229	1118	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	77.301	228	1118	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	77.3005	228	1118	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	77.259	254	1118	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	77.2215	224	1118	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	77.1565	197	1118	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	77.0993	195	1118	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	76.977	242	1118	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	76.8799	169	1118	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	76.8749	163	1118	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	76.4715	183	1118	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	76.3705	182	1118	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:52:52,598] [INFO] DFAST Taxonomy check result was written to GCA_002404345.1_ASM240434v1_genomic.fna/tc_result.tsv
[2023-06-26 23:52:52,599] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:52:52,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:52:52,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference/checkm_data
[2023-06-26 23:52:52,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:52:52,643] [INFO] Task started: CheckM
[2023-06-26 23:52:52,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002404345.1_ASM240434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002404345.1_ASM240434v1_genomic.fna/checkm_input GCA_002404345.1_ASM240434v1_genomic.fna/checkm_result
[2023-06-26 23:53:26,813] [INFO] Task succeeded: CheckM
[2023-06-26 23:53:26,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:53:26,837] [INFO] ===== Completeness check finished =====
[2023-06-26 23:53:26,838] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:53:26,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002404345.1_ASM240434v1_genomic.fna/markers.fasta)
[2023-06-26 23:53:26,838] [INFO] Task started: Blastn
[2023-06-26 23:53:26,839] [INFO] Running command: blastn -query GCA_002404345.1_ASM240434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25811380-3dd8-46e4-80b9-b3d76e4748ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_002404345.1_ASM240434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:53:27,952] [INFO] Task succeeded: Blastn
[2023-06-26 23:53:27,957] [INFO] Selected 10 target genomes.
[2023-06-26 23:53:27,957] [INFO] Target genome list was writen to GCA_002404345.1_ASM240434v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:53:27,979] [INFO] Task started: fastANI
[2023-06-26 23:53:27,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg1648db04-a2b0-4775-8461-3bb0d3c618d9/GCA_002404345.1_ASM240434v1_genomic.fna.gz --refList GCA_002404345.1_ASM240434v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002404345.1_ASM240434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:53:35,495] [INFO] Task succeeded: fastANI
[2023-06-26 23:53:35,512] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:53:35,512] [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
GCA_002404345.1	s__UBA4719 sp002404345	99.9999	1101	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014377705.1	s__UBA4719 sp014377705	82.3707	570	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132125.1	s__UBA4719 sp003132125	82.1625	500	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927555.1	s__UBA4719 sp012927555	81.9447	581	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	99.32	99.32	0.85	0.85	2	-
GCA_003157445.1	s__UBA4719 sp003157445	80.7166	443	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.5457	438	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438965.1	s__Pedococcus bigeumensis	78.1115	325	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	77.5362	253	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190805.1	s__Flexivirga oryzae	77.3012	229	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838445.1	s__F2B08 sp012838445	77.1356	193	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__F2B08	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:53:35,514] [INFO] GTDB search result was written to GCA_002404345.1_ASM240434v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:53:35,514] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:53:35,606] [INFO] DFAST_QC result json was written to GCA_002404345.1_ASM240434v1_genomic.fna/dqc_result.json
[2023-06-26 23:53:35,607] [INFO] DFAST_QC completed!
[2023-06-26 23:53:35,607] [INFO] Total running time: 0h1m14s