[2024-01-24 12:52:51,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference
[2024-01-24 12:52:53,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,753] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d80afb9-b1d9-471c-bd53-0143892030e7/GCF_007752535.1_ASM775253v1_genomic.fna.gz | prodigal -d GCF_007752535.1_ASM775253v1_genomic.fna/cds.fna -a GCF_007752535.1_ASM775253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:16,706] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:16,706] [INFO] Task started: HMMsearch
[2024-01-24 12:53:16,707] [INFO] Running command: hmmsearch --tblout GCF_007752535.1_ASM775253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference/reference_markers.hmm GCF_007752535.1_ASM775253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:17,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:17,082] [INFO] Found 6/6 markers.
[2024-01-24 12:53:17,150] [INFO] Query marker FASTA was written to GCF_007752535.1_ASM775253v1_genomic.fna/markers.fasta
[2024-01-24 12:53:17,150] [INFO] Task started: Blastn
[2024-01-24 12:53:17,151] [INFO] Running command: blastn -query GCF_007752535.1_ASM775253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference/reference_markers.fasta -out GCF_007752535.1_ASM775253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:17,818] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:17,822] [INFO] Selected 19 target genomes.
[2024-01-24 12:53:17,823] [INFO] Target genome list was writen to GCF_007752535.1_ASM775253v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:17,843] [INFO] Task started: fastANI
[2024-01-24 12:53:17,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d80afb9-b1d9-471c-bd53-0143892030e7/GCF_007752535.1_ASM775253v1_genomic.fna.gz --refList GCF_007752535.1_ASM775253v1_genomic.fna/target_genomes.txt --output GCF_007752535.1_ASM775253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:46,073] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:46,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:46,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:46,091] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:46,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:46,091] [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
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	100.0	3123	3128	95	conclusive
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	82.1885	1537	3128	95	below_threshold
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	79.2365	1085	3128	95	below_threshold
Tautonia rosea	strain=JC657	GCA_012958305.1	2728037	2728037	type	True	78.8577	988	3128	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	77.105	694	3128	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	77.0313	920	3128	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	76.9095	606	3128	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	76.8898	949	3128	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	74.9103	149	3128	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	74.802	182	3128	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	74.781	196	3128	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	74.7804	374	3128	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	74.7654	269	3128	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	74.731	399	3128	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	74.7135	427	3128	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	74.6885	380	3128	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	74.6758	421	3128	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	74.6575	490	3128	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	74.619	180	3128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:46,093] [INFO] DFAST Taxonomy check result was written to GCF_007752535.1_ASM775253v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:46,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:46,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:46,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference/checkm_data
[2024-01-24 12:53:46,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:46,194] [INFO] Task started: CheckM
[2024-01-24 12:53:46,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007752535.1_ASM775253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007752535.1_ASM775253v1_genomic.fna/checkm_input GCF_007752535.1_ASM775253v1_genomic.fna/checkm_result
[2024-01-24 12:55:04,159] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:04,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:04,194] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:04,194] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:04,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007752535.1_ASM775253v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:04,195] [INFO] Task started: Blastn
[2024-01-24 12:55:04,195] [INFO] Running command: blastn -query GCF_007752535.1_ASM775253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb98f3e93-83d2-4e0a-8a5a-a69a426873ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_007752535.1_ASM775253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:05,220] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:05,226] [INFO] Selected 13 target genomes.
[2024-01-24 12:55:05,226] [INFO] Target genome list was writen to GCF_007752535.1_ASM775253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:05,273] [INFO] Task started: fastANI
[2024-01-24 12:55:05,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d80afb9-b1d9-471c-bd53-0143892030e7/GCF_007752535.1_ASM775253v1_genomic.fna.gz --refList GCF_007752535.1_ASM775253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007752535.1_ASM775253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:27,498] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:27,511] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:27,512] [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
GCF_007752535.1	s__Tautonia plasticadhaerens	100.0	3123	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003977685.1	s__Tautonia sociabilis	82.1935	1536	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177065.1	s__Tautonia marina	79.2353	1086	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012958305.1	s__Tautonia rosea	78.8902	979	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	100.00	100.00	1.00	1.00	3	-
GCA_019232645.1	s__JAFANO01 sp019232645	77.4673	392	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__JAFANO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610895.1	s__Paludisphaera sp001610895	77.1083	816	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956985.1	s__Paludisphaera borealis	77.0909	694	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	77.0636	871	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	77.0502	909	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	76.8906	947	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064615.1	s__Aquisphaera sp011064615	76.8276	790	3128	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009785715.1	s__WQVT01 sp009785715	74.8926	94	3128	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__WQVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225825.1	s__Brachybacterium squillarum	74.7746	202	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:27,514] [INFO] GTDB search result was written to GCF_007752535.1_ASM775253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:27,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:27,519] [INFO] DFAST_QC result json was written to GCF_007752535.1_ASM775253v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:27,519] [INFO] DFAST_QC completed!
[2024-01-24 12:55:27,519] [INFO] Total running time: 0h2m36s