[2024-01-24 14:39:15,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference
[2024-01-24 14:39:17,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:17,014] [INFO] Task started: Prodigal
[2024-01-24 14:39:17,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgcecdaba3-6895-405b-bf94-9abde87e55b3/GCF_016734765.1_ASM1673476v1_genomic.fna.gz | prodigal -d GCF_016734765.1_ASM1673476v1_genomic.fna/cds.fna -a GCF_016734765.1_ASM1673476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:36,178] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:36,178] [INFO] Task started: HMMsearch
[2024-01-24 14:39:36,178] [INFO] Running command: hmmsearch --tblout GCF_016734765.1_ASM1673476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference/reference_markers.hmm GCF_016734765.1_ASM1673476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:36,497] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:36,499] [INFO] Found 6/6 markers.
[2024-01-24 14:39:36,559] [INFO] Query marker FASTA was written to GCF_016734765.1_ASM1673476v1_genomic.fna/markers.fasta
[2024-01-24 14:39:36,560] [INFO] Task started: Blastn
[2024-01-24 14:39:36,560] [INFO] Running command: blastn -query GCF_016734765.1_ASM1673476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference/reference_markers.fasta -out GCF_016734765.1_ASM1673476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:37,721] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:37,726] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:37,726] [INFO] Target genome list was writen to GCF_016734765.1_ASM1673476v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:37,733] [INFO] Task started: fastANI
[2024-01-24 14:39:37,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgcecdaba3-6895-405b-bf94-9abde87e55b3/GCF_016734765.1_ASM1673476v1_genomic.fna.gz --refList GCF_016734765.1_ASM1673476v1_genomic.fna/target_genomes.txt --output GCF_016734765.1_ASM1673476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:00,727] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:00,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:00,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:00,740] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:00,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:00,741] [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
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	100.0	2004	2012	95	conclusive
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	87.9645	1365	2012	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	87.7097	1300	2012	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.3314	1201	2012	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	84.1653	1070	2012	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.1421	1269	2012	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	83.9819	1121	2012	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	83.7561	1166	2012	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.5028	905	2012	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.4927	934	2012	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.3616	831	2012	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.1859	921	2012	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	81.7112	925	2012	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	79.8205	706	2012	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.1767	528	2012	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.1178	483	2012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:00,743] [INFO] DFAST Taxonomy check result was written to GCF_016734765.1_ASM1673476v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:00,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:00,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:00,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference/checkm_data
[2024-01-24 14:40:00,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:00,805] [INFO] Task started: CheckM
[2024-01-24 14:40:00,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016734765.1_ASM1673476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016734765.1_ASM1673476v1_genomic.fna/checkm_input GCF_016734765.1_ASM1673476v1_genomic.fna/checkm_result
[2024-01-24 14:40:52,434] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:52,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:52,454] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:52,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:52,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016734765.1_ASM1673476v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:52,455] [INFO] Task started: Blastn
[2024-01-24 14:40:52,455] [INFO] Running command: blastn -query GCF_016734765.1_ASM1673476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639fee56-d6f9-4051-a7e7-18e107ee6cc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016734765.1_ASM1673476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:54,421] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:54,424] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:54,424] [INFO] Target genome list was writen to GCF_016734765.1_ASM1673476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:54,432] [INFO] Task started: fastANI
[2024-01-24 14:40:54,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgcecdaba3-6895-405b-bf94-9abde87e55b3/GCF_016734765.1_ASM1673476v1_genomic.fna.gz --refList GCF_016734765.1_ASM1673476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016734765.1_ASM1673476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:12,356] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:12,366] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:12,366] [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_016734765.1	s__Microvirga soli	100.0	2004	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014699075.1	s__Microvirga sp014699075	88.8656	1448	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739015.1	s__Microvirga sp000739015	88.3524	1349	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694425.1	s__Microvirga sp015694425	88.1942	1176	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811235.1	s__Microvirga arabica	88.009	1361	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191055.1	s__Microvirga lupini_A	87.8642	1255	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427565.1	s__Microvirga sp016427565	87.6996	1301	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892765.1	s__Microvirga sp016892765	86.2728	1341	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743775.1	s__Microvirga aerilata	84.3266	1201	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741015.1	s__Microvirga ossetica	84.1375	1269	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735695.1	s__Microvirga zambiensis	83.9737	1122	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004458765.1	s__Microvirga pakistanensis	82.5097	932	2012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:12,368] [INFO] GTDB search result was written to GCF_016734765.1_ASM1673476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:12,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:12,385] [INFO] DFAST_QC result json was written to GCF_016734765.1_ASM1673476v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:12,385] [INFO] DFAST_QC completed!
[2024-01-24 14:41:12,385] [INFO] Total running time: 0h1m57s