[2024-01-24 15:19:03,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:03,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:03,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference
[2024-01-24 15:19:04,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:04,971] [INFO] Task started: Prodigal
[2024-01-24 15:19:04,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b1632b3-66b9-47df-b8f6-14a6cb9f8f8b/GCF_016735695.1_ASM1673569v1_genomic.fna.gz | prodigal -d GCF_016735695.1_ASM1673569v1_genomic.fna/cds.fna -a GCF_016735695.1_ASM1673569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:25,572] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:25,572] [INFO] Task started: HMMsearch
[2024-01-24 15:19:25,572] [INFO] Running command: hmmsearch --tblout GCF_016735695.1_ASM1673569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference/reference_markers.hmm GCF_016735695.1_ASM1673569v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:25,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:25,912] [INFO] Found 6/6 markers.
[2024-01-24 15:19:25,973] [INFO] Query marker FASTA was written to GCF_016735695.1_ASM1673569v1_genomic.fna/markers.fasta
[2024-01-24 15:19:25,973] [INFO] Task started: Blastn
[2024-01-24 15:19:25,973] [INFO] Running command: blastn -query GCF_016735695.1_ASM1673569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference/reference_markers.fasta -out GCF_016735695.1_ASM1673569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:27,061] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:27,069] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:27,070] [INFO] Target genome list was writen to GCF_016735695.1_ASM1673569v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:27,076] [INFO] Task started: fastANI
[2024-01-24 15:19:27,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1632b3-66b9-47df-b8f6-14a6cb9f8f8b/GCF_016735695.1_ASM1673569v1_genomic.fna.gz --refList GCF_016735695.1_ASM1673569v1_genomic.fna/target_genomes.txt --output GCF_016735695.1_ASM1673569v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:54,350] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:54,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:54,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:54,375] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:54,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:54,375] [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 zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	100.0	2327	2336	95	conclusive
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	88.1521	1593	2336	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	85.139	1325	2336	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	84.8586	1168	2336	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	84.6515	1059	2336	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	84.5102	1305	2336	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	84.0656	1076	2336	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	84.0293	1116	2336	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	83.6655	1095	2336	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.6391	899	2336	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.4418	937	2336	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.4233	864	2336	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.2307	948	2336	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	82.1708	1015	2336	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	81.7978	903	2336	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	79.8216	721	2336	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.5612	595	2336	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.3644	607	2336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:54,377] [INFO] DFAST Taxonomy check result was written to GCF_016735695.1_ASM1673569v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:54,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:54,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:54,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference/checkm_data
[2024-01-24 15:19:54,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:54,450] [INFO] Task started: CheckM
[2024-01-24 15:19:54,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016735695.1_ASM1673569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016735695.1_ASM1673569v1_genomic.fna/checkm_input GCF_016735695.1_ASM1673569v1_genomic.fna/checkm_result
[2024-01-24 15:20:54,577] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:54,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:54,602] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:54,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:54,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016735695.1_ASM1673569v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:54,604] [INFO] Task started: Blastn
[2024-01-24 15:20:54,604] [INFO] Running command: blastn -query GCF_016735695.1_ASM1673569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg733d4d8c-6afc-45ed-ae1f-f29a570d01c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016735695.1_ASM1673569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:56,751] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:56,755] [INFO] Selected 15 target genomes.
[2024-01-24 15:20:56,756] [INFO] Target genome list was writen to GCF_016735695.1_ASM1673569v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:56,768] [INFO] Task started: fastANI
[2024-01-24 15:20:56,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1632b3-66b9-47df-b8f6-14a6cb9f8f8b/GCF_016735695.1_ASM1673569v1_genomic.fna.gz --refList GCF_016735695.1_ASM1673569v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016735695.1_ASM1673569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:22,682] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:22,700] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:22,700] [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_016735695.1	s__Microvirga zambiensis	100.0	2327	2336	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_002741015.1	s__Microvirga ossetica	88.1256	1597	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864375.1	s__Microvirga sp016864375	84.9199	1442	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383585.1	s__Microvirga sp018383585	84.9155	1179	2336	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	84.8525	1169	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	84.6732	1050	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016427565.1	s__Microvirga sp016427565	84.6646	1058	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000517005.1	s__Microvirga lupini	84.5657	1392	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	84.5208	1300	2336	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	84.4291	1144	2336	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	84.3679	1058	2336	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	84.2169	1088	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699075.1	s__Microvirga sp014699075	83.8491	1132	2336	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	82.472	932	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830105.1	s__Microvirga makkahensis	81.8028	902	2336	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 15:21:22,702] [INFO] GTDB search result was written to GCF_016735695.1_ASM1673569v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:22,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:22,706] [INFO] DFAST_QC result json was written to GCF_016735695.1_ASM1673569v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:22,706] [INFO] DFAST_QC completed!
[2024-01-24 15:21:22,706] [INFO] Total running time: 0h2m19s