[2024-01-24 11:12:56,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:56,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:56,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference
[2024-01-24 11:12:58,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:58,086] [INFO] Task started: Prodigal
[2024-01-24 11:12:58,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dc28499-3458-4d2f-84f4-a0040f5e69bd/GCF_004364555.1_ASM436455v1_genomic.fna.gz | prodigal -d GCF_004364555.1_ASM436455v1_genomic.fna/cds.fna -a GCF_004364555.1_ASM436455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:08,223] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:08,224] [INFO] Task started: HMMsearch
[2024-01-24 11:13:08,224] [INFO] Running command: hmmsearch --tblout GCF_004364555.1_ASM436455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference/reference_markers.hmm GCF_004364555.1_ASM436455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:08,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:08,546] [INFO] Found 6/6 markers.
[2024-01-24 11:13:08,596] [INFO] Query marker FASTA was written to GCF_004364555.1_ASM436455v1_genomic.fna/markers.fasta
[2024-01-24 11:13:08,597] [INFO] Task started: Blastn
[2024-01-24 11:13:08,597] [INFO] Running command: blastn -query GCF_004364555.1_ASM436455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference/reference_markers.fasta -out GCF_004364555.1_ASM436455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:10,073] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:10,075] [INFO] Selected 23 target genomes.
[2024-01-24 11:13:10,076] [INFO] Target genome list was writen to GCF_004364555.1_ASM436455v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:10,084] [INFO] Task started: fastANI
[2024-01-24 11:13:10,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc28499-3458-4d2f-84f4-a0040f5e69bd/GCF_004364555.1_ASM436455v1_genomic.fna.gz --refList GCF_004364555.1_ASM436455v1_genomic.fna/target_genomes.txt --output GCF_004364555.1_ASM436455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:26,918] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:26,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:26,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:26,936] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:26,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:26,936] [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
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	100.0	1233	1233	95	conclusive
Amnibacterium setariae	strain=DD4a	GCA_003581425.1	2306585	2306585	type	True	85.3681	887	1233	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.537	431	1233	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.5286	437	1233	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.4378	513	1233	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.4261	431	1233	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.4248	463	1233	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.419	457	1233	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3407	468	1233	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	78.282	472	1233	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	78.2271	470	1233	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.2234	436	1233	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.2015	429	1233	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	78.152	435	1233	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	78.0787	445	1233	95	below_threshold
Curtobacterium citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	78.0234	449	1233	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	78.0171	409	1233	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	78.0135	418	1233	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	77.8701	412	1233	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	77.6745	384	1233	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	77.5018	384	1233	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	77.4921	360	1233	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	77.4052	374	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:26,937] [INFO] DFAST Taxonomy check result was written to GCF_004364555.1_ASM436455v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:26,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:26,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:26,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference/checkm_data
[2024-01-24 11:13:26,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:26,978] [INFO] Task started: CheckM
[2024-01-24 11:13:26,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364555.1_ASM436455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364555.1_ASM436455v1_genomic.fna/checkm_input GCF_004364555.1_ASM436455v1_genomic.fna/checkm_result
[2024-01-24 11:14:15,457] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:15,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:15,479] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:15,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:15,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364555.1_ASM436455v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:15,480] [INFO] Task started: Blastn
[2024-01-24 11:14:15,480] [INFO] Running command: blastn -query GCF_004364555.1_ASM436455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8259387c-837b-4c15-82bc-6438dd732cf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364555.1_ASM436455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:17,819] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:17,823] [INFO] Selected 23 target genomes.
[2024-01-24 11:14:17,824] [INFO] Target genome list was writen to GCF_004364555.1_ASM436455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:17,850] [INFO] Task started: fastANI
[2024-01-24 11:14:17,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc28499-3458-4d2f-84f4-a0040f5e69bd/GCF_004364555.1_ASM436455v1_genomic.fna.gz --refList GCF_004364555.1_ASM436455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364555.1_ASM436455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:35,392] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:35,413] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:35,413] [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_004364555.1	s__Amnibacterium kyonggiense	100.0	1233	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003581425.1	s__Amnibacterium setariae	85.4149	883	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384945.1	s__Clavibacter sp003384945	78.5119	455	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011135.1	s__Rathayibacter festucae	78.4747	509	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
GCF_009866655.1	s__Rathayibacter sp009866655	78.4253	503	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_006517535.1	s__Schumannella sp006517535	78.3493	441	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	78.3237	470	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001705035.1	s__Curtobacterium sp001705035	78.3168	428	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.77	98.72	0.93	0.91	3	-
GCF_013205055.1	s__Rathayibacter sp013205055	78.2996	511	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003627075.1	s__Protaetiibacter intestinalis	78.2187	427	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759585.1	s__Frigoribacterium endophyticum	78.2126	473	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_017833035.1	s__Frigoribacterium sp017833035	78.1641	465	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	78.159	443	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806325.1	s__Curtobacterium sp001806325	78.1545	426	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_004959775.1	s__Agromyces sp004959775	78.0967	442	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765225.1	s__Leifsonia sp009765225	78.0768	398	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923295.1	s__Agrococcus sediminis	78.0375	416	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	-
GCF_003634555.1	s__Frondihabitans australicus	78.0272	417	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627055.1	s__Gryllotalpicola protaetiae	78.0169	409	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	78.012	463	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364285.1	s__Frigoribacterium sp004364285	77.9513	483	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	96.77	95.63	0.92	0.87	5	-
GCF_900104705.1	s__Agrococcus carbonis	77.8536	414	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759705.1	s__Microbacterium ulmi	77.413	373	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:35,415] [INFO] GTDB search result was written to GCF_004364555.1_ASM436455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:35,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:35,419] [INFO] DFAST_QC result json was written to GCF_004364555.1_ASM436455v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:35,420] [INFO] DFAST_QC completed!
[2024-01-24 11:14:35,420] [INFO] Total running time: 0h1m39s