[2024-01-24 13:40:43,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference
[2024-01-24 13:40:45,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,111] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg1322509f-fb5b-4485-ba51-bc7bd28ad8e7/GCF_003253475.1_ASM325347v1_genomic.fna.gz | prodigal -d GCF_003253475.1_ASM325347v1_genomic.fna/cds.fna -a GCF_003253475.1_ASM325347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:04,822] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:04,823] [INFO] Task started: HMMsearch
[2024-01-24 13:41:04,823] [INFO] Running command: hmmsearch --tblout GCF_003253475.1_ASM325347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference/reference_markers.hmm GCF_003253475.1_ASM325347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:05,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:05,146] [INFO] Found 6/6 markers.
[2024-01-24 13:41:05,199] [INFO] Query marker FASTA was written to GCF_003253475.1_ASM325347v1_genomic.fna/markers.fasta
[2024-01-24 13:41:05,199] [INFO] Task started: Blastn
[2024-01-24 13:41:05,200] [INFO] Running command: blastn -query GCF_003253475.1_ASM325347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference/reference_markers.fasta -out GCF_003253475.1_ASM325347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,397] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,400] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:06,401] [INFO] Target genome list was writen to GCF_003253475.1_ASM325347v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:06,406] [INFO] Task started: fastANI
[2024-01-24 13:41:06,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg1322509f-fb5b-4485-ba51-bc7bd28ad8e7/GCF_003253475.1_ASM325347v1_genomic.fna.gz --refList GCF_003253475.1_ASM325347v1_genomic.fna/target_genomes.txt --output GCF_003253475.1_ASM325347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:29,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:29,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:29,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:29,475] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:29,475] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:29,476] [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
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	100.0	2149	2150	95	conclusive
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	99.9943	2142	2150	95	conclusive
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	99.9756	2094	2150	95	conclusive
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	89.9465	1600	2150	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	88.3909	1388	2150	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	86.8959	1391	2150	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	86.265	1529	2150	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.9833	1034	2150	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	84.2299	1285	2150	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.833	1203	2150	95	below_threshold
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	83.591	1263	2150	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.4538	1323	2150	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.3065	1344	2150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:29,477] [INFO] DFAST Taxonomy check result was written to GCF_003253475.1_ASM325347v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:29,478] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:29,478] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:29,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference/checkm_data
[2024-01-24 13:41:29,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:29,543] [INFO] Task started: CheckM
[2024-01-24 13:41:29,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253475.1_ASM325347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253475.1_ASM325347v1_genomic.fna/checkm_input GCF_003253475.1_ASM325347v1_genomic.fna/checkm_result
[2024-01-24 13:42:35,712] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:35,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:35,744] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:35,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:35,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253475.1_ASM325347v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:35,745] [INFO] Task started: Blastn
[2024-01-24 13:42:35,745] [INFO] Running command: blastn -query GCF_003253475.1_ASM325347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0736830-3c66-49dd-80bb-5c3cccd4ef95/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253475.1_ASM325347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:37,548] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:37,551] [INFO] Selected 20 target genomes.
[2024-01-24 13:42:37,552] [INFO] Target genome list was writen to GCF_003253475.1_ASM325347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:37,575] [INFO] Task started: fastANI
[2024-01-24 13:42:37,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg1322509f-fb5b-4485-ba51-bc7bd28ad8e7/GCF_003253475.1_ASM325347v1_genomic.fna.gz --refList GCF_003253475.1_ASM325347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253475.1_ASM325347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:12,847] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:12,877] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:12,878] [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_900109115.1	s__Micromonospora phaseoli	99.9943	2142	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003236315.1	s__Micromonospora craterilacus	88.4234	1385	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010560025.1	s__Micromonospora sp010560025	88.0423	1569	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_900112325.1	s__Micromonospora sediminimaris	88.0145	1610	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
GCF_018070465.1	s__Micromonospora sp018070465	87.9308	1599	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005402585.1	s__Micromonospora sp005402585	87.9239	1569	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863495.1	s__Micromonospora andamanensis	87.8568	1634	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_016863535.1	s__Micromonospora lutea	87.6207	1523	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863555.1	s__Micromonospora qiuiae	86.9425	1379	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646235.1	s__Micromonospora sonchi	86.9056	1430	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764405.1	s__Micromonospora craniellae	86.8462	1416	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_003236305.1	s__Micromonospora endophytica	86.5908	1286	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	84.7882	1413	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900091445.1	s__Micromonospora echinofusca	84.3544	1350	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_003626595.1	s__Micromonospora endolithica	84.2613	1421	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	84.1734	1293	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_003434305.1	s__Micromonospora sp003434305	83.9168	1240	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348595.1	s__Micromonospora sp004348595	83.6815	1150	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908295.1	s__Micromonospora rubida	83.5583	1267	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348325.1	s__Micromonospora sp004348325	83.3602	1132	2150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.89	97.89	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:12,881] [INFO] GTDB search result was written to GCF_003253475.1_ASM325347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:12,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:12,887] [INFO] DFAST_QC result json was written to GCF_003253475.1_ASM325347v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:12,887] [INFO] DFAST_QC completed!
[2024-01-24 13:43:12,888] [INFO] Total running time: 0h2m29s