[2024-01-24 11:51:10,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference
[2024-01-24 11:51:11,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,664] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg1240beb6-4724-4efb-8d3f-f69ed9bab1bd/GCF_030296595.1_ASM3029659v1_genomic.fna.gz | prodigal -d GCF_030296595.1_ASM3029659v1_genomic.fna/cds.fna -a GCF_030296595.1_ASM3029659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:21,071] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:21,071] [INFO] Task started: HMMsearch
[2024-01-24 11:51:21,071] [INFO] Running command: hmmsearch --tblout GCF_030296595.1_ASM3029659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference/reference_markers.hmm GCF_030296595.1_ASM3029659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:21,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:21,360] [INFO] Found 6/6 markers.
[2024-01-24 11:51:21,390] [INFO] Query marker FASTA was written to GCF_030296595.1_ASM3029659v1_genomic.fna/markers.fasta
[2024-01-24 11:51:21,390] [INFO] Task started: Blastn
[2024-01-24 11:51:21,390] [INFO] Running command: blastn -query GCF_030296595.1_ASM3029659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference/reference_markers.fasta -out GCF_030296595.1_ASM3029659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:22,617] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:22,620] [INFO] Selected 36 target genomes.
[2024-01-24 11:51:22,621] [INFO] Target genome list was writen to GCF_030296595.1_ASM3029659v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:22,632] [INFO] Task started: fastANI
[2024-01-24 11:51:22,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg1240beb6-4724-4efb-8d3f-f69ed9bab1bd/GCF_030296595.1_ASM3029659v1_genomic.fna.gz --refList GCF_030296595.1_ASM3029659v1_genomic.fna/target_genomes.txt --output GCF_030296595.1_ASM3029659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,708] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,739] [INFO] Found 36 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:46,739] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:46,740] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.5239	395	1130	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	79.4583	300	1130	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.4368	311	1130	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.3521	406	1130	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.3308	426	1130	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.3056	413	1130	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.2531	409	1130	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	79.2528	321	1130	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.2265	349	1130	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.1334	471	1130	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.1236	407	1130	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	79.0772	417	1130	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	79.064	410	1130	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	79.0638	369	1130	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	78.9899	433	1130	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.9747	415	1130	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	78.9466	388	1130	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.9154	463	1130	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	78.9147	443	1130	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.9047	450	1130	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	78.9032	410	1130	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	78.833	341	1130	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	78.8234	388	1130	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	78.7295	427	1130	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	78.6488	337	1130	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	78.5917	340	1130	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	78.5631	320	1130	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.5587	366	1130	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	78.4393	350	1130	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.4076	379	1130	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	78.39	359	1130	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.3617	382	1130	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.3057	309	1130	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	78.0226	253	1130	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	77.8298	299	1130	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	77.79	274	1130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,743] [INFO] DFAST Taxonomy check result was written to GCF_030296595.1_ASM3029659v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference/checkm_data
[2024-01-24 11:51:46,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,781] [INFO] Task started: CheckM
[2024-01-24 11:51:46,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296595.1_ASM3029659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296595.1_ASM3029659v1_genomic.fna/checkm_input GCF_030296595.1_ASM3029659v1_genomic.fna/checkm_result
[2024-01-24 11:52:29,218] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:29,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,242] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:29,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:29,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296595.1_ASM3029659v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:29,243] [INFO] Task started: Blastn
[2024-01-24 11:52:29,243] [INFO] Running command: blastn -query GCF_030296595.1_ASM3029659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec1d064-cec8-4a8b-a9d2-ae927ae8f862/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296595.1_ASM3029659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:31,225] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:31,230] [INFO] Selected 25 target genomes.
[2024-01-24 11:52:31,230] [INFO] Target genome list was writen to GCF_030296595.1_ASM3029659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:31,288] [INFO] Task started: fastANI
[2024-01-24 11:52:31,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg1240beb6-4724-4efb-8d3f-f69ed9bab1bd/GCF_030296595.1_ASM3029659v1_genomic.fna.gz --refList GCF_030296595.1_ASM3029659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296595.1_ASM3029659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:47,830] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:47,849] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:47,850] [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_017916505.1	s__Naasia sp017916505	82.9301	697	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916515.1	s__Naasia sp017916515	81.8427	612	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801885.1	s__Naasia lichenicola	80.0575	517	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097495.1	s__Naasia flavum	79.6741	453	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.4681	399	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280205.1	s__Clavibacter capsici	79.3782	394	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCF_002240635.1	s__Clavibacter tessellarius	79.37	422	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.2907	432	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355695.1	s__Clavibacter nebraskensis	79.2818	407	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.97	99.95	1.00	1.00	6	-
GCA_001725325.1	s__Rhodoglobus sp001725325	79.1845	416	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004011135.1	s__Rathayibacter festucae	79.164	475	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
GCF_001647635.1	s__Leifsonia xyli_A	79.078	430	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168345.1	s__Clavibacter michiganensis	79.0633	410	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCF_009765225.1	s__Leifsonia sp009765225	79.0273	387	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710805.1	s__Agromyces tardus	78.9539	439	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517535.1	s__Schumannella sp006517535	78.9221	411	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	78.8808	387	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	78.8773	413	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_008122505.1	s__Agromyces sp008122505	78.8768	467	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633535.1	s__Leifsonia aquatica_A	78.8247	394	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759585.1	s__Frigoribacterium endophyticum	78.7628	419	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_009709675.1	s__Agromyces bracchium	78.7292	427	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645235.1	s__Agrococcus terreus	78.5235	346	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204985.1	s__Rathayibacter sp013204985	78.1561	374	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691565.1	s__Microbacterium oleivorans_B	77.9403	286	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:47,851] [INFO] GTDB search result was written to GCF_030296595.1_ASM3029659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:47,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:47,857] [INFO] DFAST_QC result json was written to GCF_030296595.1_ASM3029659v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:47,857] [INFO] DFAST_QC completed!
[2024-01-24 11:52:47,858] [INFO] Total running time: 0h1m37s