[2024-01-24 10:47:06,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,552] [INFO] DQC Reference Directory: /var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference
[2024-01-24 10:47:12,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,103] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgef893fc1-ec07-4b0a-8b4a-f7116c8e0c2f/GCF_015694425.1_ASM1569442v1_genomic.fna.gz | prodigal -d GCF_015694425.1_ASM1569442v1_genomic.fna/cds.fna -a GCF_015694425.1_ASM1569442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,215] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,215] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,215] [INFO] Running command: hmmsearch --tblout GCF_015694425.1_ASM1569442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference/reference_markers.hmm GCF_015694425.1_ASM1569442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,467] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,468] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,523] [INFO] Query marker FASTA was written to GCF_015694425.1_ASM1569442v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,524] [INFO] Task started: Blastn
[2024-01-24 10:47:24,524] [INFO] Running command: blastn -query GCF_015694425.1_ASM1569442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference/reference_markers.fasta -out GCF_015694425.1_ASM1569442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,605] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,609] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:25,609] [INFO] Target genome list was writen to GCF_015694425.1_ASM1569442v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,638] [INFO] Task started: fastANI
[2024-01-24 10:47:25,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgef893fc1-ec07-4b0a-8b4a-f7116c8e0c2f/GCF_015694425.1_ASM1569442v1_genomic.fna.gz --refList GCF_015694425.1_ASM1569442v1_genomic.fna/target_genomes.txt --output GCF_015694425.1_ASM1569442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:48,812] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:48,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:48,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:48,832] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:48,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:48,833] [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 arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	88.4394	1131	1392	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	88.245	1175	1392	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	87.5536	1124	1392	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.4535	1038	1392	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	84.3182	915	1392	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.2966	990	1392	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.1225	1012	1392	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	84.0569	991	1392	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	83.9497	1002	1392	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.5004	843	1392	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.1432	857	1392	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.081	815	1392	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.0472	817	1392	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	81.6466	791	1392	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	80.0473	627	1392	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	78.909	525	1392	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.2969	417	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:48,835] [INFO] DFAST Taxonomy check result was written to GCF_015694425.1_ASM1569442v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:48,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:48,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:48,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference/checkm_data
[2024-01-24 10:47:48,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:48,888] [INFO] Task started: CheckM
[2024-01-24 10:47:48,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015694425.1_ASM1569442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015694425.1_ASM1569442v1_genomic.fna/checkm_input GCF_015694425.1_ASM1569442v1_genomic.fna/checkm_result
[2024-01-24 10:48:27,367] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:27,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,383] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:27,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:27,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015694425.1_ASM1569442v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:27,384] [INFO] Task started: Blastn
[2024-01-24 10:48:27,384] [INFO] Running command: blastn -query GCF_015694425.1_ASM1569442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2f17a47-79c7-4436-8568-4c7bf4fc359e/dqc_reference/reference_markers_gtdb.fasta -out GCF_015694425.1_ASM1569442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:29,175] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:29,178] [INFO] Selected 10 target genomes.
[2024-01-24 10:48:29,179] [INFO] Target genome list was writen to GCF_015694425.1_ASM1569442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:29,202] [INFO] Task started: fastANI
[2024-01-24 10:48:29,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgef893fc1-ec07-4b0a-8b4a-f7116c8e0c2f/GCF_015694425.1_ASM1569442v1_genomic.fna.gz --refList GCF_015694425.1_ASM1569442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015694425.1_ASM1569442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:42,258] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:42,267] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:42,267] [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_015694425.1	s__Microvirga sp015694425	100.0	1390	1392	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	89.0603	1185	1392	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	88.6359	1174	1392	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	88.4394	1131	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734765.1	s__Microvirga soli	88.2427	1175	1392	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	87.7135	1187	1392	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	87.5209	1127	1392	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	85.9137	1114	1392	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	84.2816	991	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	84.0531	992	1392	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 10:48:42,269] [INFO] GTDB search result was written to GCF_015694425.1_ASM1569442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:42,269] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:42,273] [INFO] DFAST_QC result json was written to GCF_015694425.1_ASM1569442v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:42,273] [INFO] DFAST_QC completed!
[2024-01-24 10:48:42,273] [INFO] Total running time: 0h1m36s