[2024-01-25 20:23:05,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:05,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:05,592] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference
[2024-01-25 20:23:06,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:06,752] [INFO] Task started: Prodigal
[2024-01-25 20:23:06,752] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa09639e-c240-49dc-971a-969bb50c27c8/GCF_009363855.1_ASM936385v1_genomic.fna.gz | prodigal -d GCF_009363855.1_ASM936385v1_genomic.fna/cds.fna -a GCF_009363855.1_ASM936385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:16,117] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:16,117] [INFO] Task started: HMMsearch
[2024-01-25 20:23:16,117] [INFO] Running command: hmmsearch --tblout GCF_009363855.1_ASM936385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference/reference_markers.hmm GCF_009363855.1_ASM936385v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:16,361] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:16,362] [INFO] Found 6/6 markers.
[2024-01-25 20:23:16,392] [INFO] Query marker FASTA was written to GCF_009363855.1_ASM936385v1_genomic.fna/markers.fasta
[2024-01-25 20:23:16,393] [INFO] Task started: Blastn
[2024-01-25 20:23:16,393] [INFO] Running command: blastn -query GCF_009363855.1_ASM936385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference/reference_markers.fasta -out GCF_009363855.1_ASM936385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:17,413] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:17,416] [INFO] Selected 13 target genomes.
[2024-01-25 20:23:17,417] [INFO] Target genome list was writen to GCF_009363855.1_ASM936385v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:17,424] [INFO] Task started: fastANI
[2024-01-25 20:23:17,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa09639e-c240-49dc-971a-969bb50c27c8/GCF_009363855.1_ASM936385v1_genomic.fna.gz --refList GCF_009363855.1_ASM936385v1_genomic.fna/target_genomes.txt --output GCF_009363855.1_ASM936385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:32,878] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:32,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:32,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:32,887] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:32,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:32,888] [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 thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	100.0	1273	1274	95	conclusive
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.7102	779	1274	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.6435	829	1274	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	82.3385	786	1274	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	81.9876	796	1274	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	81.9316	794	1274	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	81.7703	741	1274	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	81.6187	789	1274	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	81.606	720	1274	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	81.543	754	1274	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	81.4319	798	1274	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	79.7156	581	1274	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.7855	548	1274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:32,889] [INFO] DFAST Taxonomy check result was written to GCF_009363855.1_ASM936385v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:32,890] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:32,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:32,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference/checkm_data
[2024-01-25 20:23:32,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:32,931] [INFO] Task started: CheckM
[2024-01-25 20:23:32,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009363855.1_ASM936385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009363855.1_ASM936385v1_genomic.fna/checkm_input GCF_009363855.1_ASM936385v1_genomic.fna/checkm_result
[2024-01-25 20:24:07,125] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:07,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:07,146] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:07,146] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:07,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009363855.1_ASM936385v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:07,148] [INFO] Task started: Blastn
[2024-01-25 20:24:07,148] [INFO] Running command: blastn -query GCF_009363855.1_ASM936385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f6ff50-2014-42dd-9edf-8fc1d1f3a14a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009363855.1_ASM936385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:09,200] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:09,203] [INFO] Selected 12 target genomes.
[2024-01-25 20:24:09,203] [INFO] Target genome list was writen to GCF_009363855.1_ASM936385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:09,235] [INFO] Task started: fastANI
[2024-01-25 20:24:09,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa09639e-c240-49dc-971a-969bb50c27c8/GCF_009363855.1_ASM936385v1_genomic.fna.gz --refList GCF_009363855.1_ASM936385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009363855.1_ASM936385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:23,819] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:23,829] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:23,830] [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_009363855.1	s__Microvirga thermotolerans	100.0	1274	1274	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_003151255.1	s__Microvirga sp003151255	85.3947	921	1274	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	82.9836	848	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003350535.1	s__Microvirga subterranea	82.6379	829	1274	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	82.3361	786	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002741015.1	s__Microvirga ossetica	81.9394	794	1274	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	81.8951	805	1274	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	81.6229	753	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	81.6227	788	1274	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	81.5929	723	1274	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	81.5354	787	1274	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	81.5349	755	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:23,831] [INFO] GTDB search result was written to GCF_009363855.1_ASM936385v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:23,832] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:23,838] [INFO] DFAST_QC result json was written to GCF_009363855.1_ASM936385v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:23,838] [INFO] DFAST_QC completed!
[2024-01-25 20:24:23,838] [INFO] Total running time: 0h1m18s