[2024-01-24 13:13:31,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:31,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:31,951] [INFO] DQC Reference Directory: /var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference
[2024-01-24 13:13:33,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:33,386] [INFO] Task started: Prodigal
[2024-01-24 13:13:33,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg549c51bc-10ef-448c-b7d8-4ec227c30521/GCF_016892765.1_ASM1689276v1_genomic.fna.gz | prodigal -d GCF_016892765.1_ASM1689276v1_genomic.fna/cds.fna -a GCF_016892765.1_ASM1689276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:52,370] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:52,371] [INFO] Task started: HMMsearch
[2024-01-24 13:13:52,371] [INFO] Running command: hmmsearch --tblout GCF_016892765.1_ASM1689276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference/reference_markers.hmm GCF_016892765.1_ASM1689276v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:52,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:52,770] [INFO] Found 6/6 markers.
[2024-01-24 13:13:52,828] [INFO] Query marker FASTA was written to GCF_016892765.1_ASM1689276v1_genomic.fna/markers.fasta
[2024-01-24 13:13:52,828] [INFO] Task started: Blastn
[2024-01-24 13:13:52,828] [INFO] Running command: blastn -query GCF_016892765.1_ASM1689276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference/reference_markers.fasta -out GCF_016892765.1_ASM1689276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:53,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:53,882] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:53,882] [INFO] Target genome list was writen to GCF_016892765.1_ASM1689276v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:53,890] [INFO] Task started: fastANI
[2024-01-24 13:13:53,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg549c51bc-10ef-448c-b7d8-4ec227c30521/GCF_016892765.1_ASM1689276v1_genomic.fna.gz --refList GCF_016892765.1_ASM1689276v1_genomic.fna/target_genomes.txt --output GCF_016892765.1_ASM1689276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:16,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:16,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:16,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:16,248] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:16,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:16,248] [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	86.2751	1340	2047	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	86.249	1181	2047	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	86.0004	1215	2047	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.742	1313	2047	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	84.7062	956	2047	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.3363	1167	2047	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.3199	1155	2047	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	84.0167	1150	2047	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.7659	882	2047	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.3786	891	2047	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.3503	830	2047	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.2793	900	2047	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	81.8526	953	2047	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.4587	530	2047	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.4403	507	2047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:16,251] [INFO] DFAST Taxonomy check result was written to GCF_016892765.1_ASM1689276v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:16,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:16,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:16,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference/checkm_data
[2024-01-24 13:14:16,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:16,320] [INFO] Task started: CheckM
[2024-01-24 13:14:16,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016892765.1_ASM1689276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016892765.1_ASM1689276v1_genomic.fna/checkm_input GCF_016892765.1_ASM1689276v1_genomic.fna/checkm_result
[2024-01-24 13:15:14,409] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:14,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:14,435] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:14,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:14,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016892765.1_ASM1689276v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:14,436] [INFO] Task started: Blastn
[2024-01-24 13:15:14,436] [INFO] Running command: blastn -query GCF_016892765.1_ASM1689276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeded1f26-6fda-490c-8723-5777ed6008ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_016892765.1_ASM1689276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:16,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:16,449] [INFO] Selected 15 target genomes.
[2024-01-24 13:15:16,449] [INFO] Target genome list was writen to GCF_016892765.1_ASM1689276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:16,472] [INFO] Task started: fastANI
[2024-01-24 13:15:16,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg549c51bc-10ef-448c-b7d8-4ec227c30521/GCF_016892765.1_ASM1689276v1_genomic.fna.gz --refList GCF_016892765.1_ASM1689276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016892765.1_ASM1689276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:37,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:37,814] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:37,815] [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_016892765.1	s__Microvirga sp016892765	100.0	2040	2047	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_016734765.1	s__Microvirga soli	86.2737	1340	2047	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	86.2693	1178	2047	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	86.0488	1210	2047	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	85.9906	1217	2047	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	85.9711	1293	2047	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	85.8368	1080	2047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015694425.1	s__Microvirga sp015694425	85.7953	1124	2047	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	85.7455	1200	2047	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	84.7647	1308	2047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518665.1	s__Microvirga flocculans	84.7368	953	2047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018383585.1	s__Microvirga sp018383585	84.5811	1087	2047	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	84.3383	1152	2047	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	84.3195	1169	2047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069605.1	s__Microvirga sp018069605	83.9481	1126	2047	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 13:15:37,816] [INFO] GTDB search result was written to GCF_016892765.1_ASM1689276v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:37,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:37,821] [INFO] DFAST_QC result json was written to GCF_016892765.1_ASM1689276v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:37,821] [INFO] DFAST_QC completed!
[2024-01-24 13:15:37,821] [INFO] Total running time: 0h2m6s