[2024-01-24 12:23:03,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference
[2024-01-24 12:23:05,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,011] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgca2d56a5-cf5a-4435-bca2-2bad16b24856/GCF_003097495.1_ASM309749v1_genomic.fna.gz | prodigal -d GCF_003097495.1_ASM309749v1_genomic.fna/cds.fna -a GCF_003097495.1_ASM309749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:14,953] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:14,954] [INFO] Task started: HMMsearch
[2024-01-24 12:23:14,954] [INFO] Running command: hmmsearch --tblout GCF_003097495.1_ASM309749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference/reference_markers.hmm GCF_003097495.1_ASM309749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:15,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:15,231] [INFO] Found 6/6 markers.
[2024-01-24 12:23:15,268] [INFO] Query marker FASTA was written to GCF_003097495.1_ASM309749v1_genomic.fna/markers.fasta
[2024-01-24 12:23:15,269] [INFO] Task started: Blastn
[2024-01-24 12:23:15,269] [INFO] Running command: blastn -query GCF_003097495.1_ASM309749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference/reference_markers.fasta -out GCF_003097495.1_ASM309749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:16,420] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:16,424] [INFO] Selected 26 target genomes.
[2024-01-24 12:23:16,425] [INFO] Target genome list was writen to GCF_003097495.1_ASM309749v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:16,433] [INFO] Task started: fastANI
[2024-01-24 12:23:16,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgca2d56a5-cf5a-4435-bca2-2bad16b24856/GCF_003097495.1_ASM309749v1_genomic.fna.gz --refList GCF_003097495.1_ASM309749v1_genomic.fna/target_genomes.txt --output GCF_003097495.1_ASM309749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:32,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:32,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:32,658] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:32,658] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:32,658] [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
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.284	398	1185	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.0695	436	1185	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	78.8671	350	1185	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	78.8524	387	1185	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.8503	376	1185	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.8251	373	1185	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	78.818	401	1185	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.7981	373	1185	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	78.6534	318	1185	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.6326	374	1185	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	78.627	404	1185	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.625	372	1185	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	78.6059	411	1185	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.6046	377	1185	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	78.6045	370	1185	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.5717	384	1185	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.5236	433	1185	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	78.4352	394	1185	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4321	344	1185	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.3959	347	1185	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.3173	398	1185	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	78.272	325	1185	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.2595	361	1185	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.2337	411	1185	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	78.127	292	1185	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	77.9445	277	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:32,660] [INFO] DFAST Taxonomy check result was written to GCF_003097495.1_ASM309749v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:32,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:32,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:32,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference/checkm_data
[2024-01-24 12:23:32,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:32,698] [INFO] Task started: CheckM
[2024-01-24 12:23:32,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003097495.1_ASM309749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003097495.1_ASM309749v1_genomic.fna/checkm_input GCF_003097495.1_ASM309749v1_genomic.fna/checkm_result
[2024-01-24 12:24:16,718] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:16,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:16,744] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:16,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:16,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003097495.1_ASM309749v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:16,746] [INFO] Task started: Blastn
[2024-01-24 12:24:16,746] [INFO] Running command: blastn -query GCF_003097495.1_ASM309749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c597771-7ad5-40fd-9082-ebe23ced758d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003097495.1_ASM309749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:18,568] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:18,573] [INFO] Selected 14 target genomes.
[2024-01-24 12:24:18,573] [INFO] Target genome list was writen to GCF_003097495.1_ASM309749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:18,585] [INFO] Task started: fastANI
[2024-01-24 12:24:18,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgca2d56a5-cf5a-4435-bca2-2bad16b24856/GCF_003097495.1_ASM309749v1_genomic.fna.gz --refList GCF_003097495.1_ASM309749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003097495.1_ASM309749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:28,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:28,729] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:28,729] [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_003097495.1	s__Naasia flavum	100.0	1184	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017916505.1	s__Naasia sp017916505	80.1047	481	1185	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	79.9845	479	1185	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	79.5461	442	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355965.1	s__JAFIQW01 sp017355965	79.3899	396	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409865.1	s__Herbiconiux flava	79.2994	396	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.1792	394	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	78.8701	385	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410355.1	s__Agromyces hippuratus	78.817	398	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003067705.1	s__Planctomonas deserti	78.8058	383	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866655.1	s__Rathayibacter sp009866655	78.7564	461	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_014190775.1	s__Leifsonia aquatica	78.4459	394	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCA_001898805.1	s__Leifsonia sp001898805	78.3275	410	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865015.1	s__Curtobacterium sp001865015	78.1436	346	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:28,731] [INFO] GTDB search result was written to GCF_003097495.1_ASM309749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:28,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:28,736] [INFO] DFAST_QC result json was written to GCF_003097495.1_ASM309749v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:28,736] [INFO] DFAST_QC completed!
[2024-01-24 12:24:28,736] [INFO] Total running time: 0h1m25s