[2024-01-24 12:44:53,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference
[2024-01-24 12:44:54,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:54,968] [INFO] Task started: Prodigal
[2024-01-24 12:44:54,968] [INFO] Running command: gunzip -c /var/lib/cwl/stge742ba1e-5826-46a3-9dd1-9a32d7f1448d/GCF_015694465.1_ASM1569446v1_genomic.fna.gz | prodigal -d GCF_015694465.1_ASM1569446v1_genomic.fna/cds.fna -a GCF_015694465.1_ASM1569446v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:08,500] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:08,500] [INFO] Task started: HMMsearch
[2024-01-24 12:45:08,500] [INFO] Running command: hmmsearch --tblout GCF_015694465.1_ASM1569446v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference/reference_markers.hmm GCF_015694465.1_ASM1569446v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:08,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:08,810] [INFO] Found 6/6 markers.
[2024-01-24 12:45:08,848] [INFO] Query marker FASTA was written to GCF_015694465.1_ASM1569446v1_genomic.fna/markers.fasta
[2024-01-24 12:45:08,849] [INFO] Task started: Blastn
[2024-01-24 12:45:08,849] [INFO] Running command: blastn -query GCF_015694465.1_ASM1569446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference/reference_markers.fasta -out GCF_015694465.1_ASM1569446v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:09,907] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:09,911] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:09,911] [INFO] Target genome list was writen to GCF_015694465.1_ASM1569446v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:09,919] [INFO] Task started: fastANI
[2024-01-24 12:45:09,919] [INFO] Running command: fastANI --query /var/lib/cwl/stge742ba1e-5826-46a3-9dd1-9a32d7f1448d/GCF_015694465.1_ASM1569446v1_genomic.fna.gz --refList GCF_015694465.1_ASM1569446v1_genomic.fna/target_genomes.txt --output GCF_015694465.1_ASM1569446v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:28,940] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:28,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:28,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:28,960] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:28,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:28,961] [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 alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	100.0	1461	1463	95	conclusive
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	81.6334	715	1463	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	81.496	668	1463	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	81.2986	653	1463	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	81.1825	748	1463	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	81.171	722	1463	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	81.1281	692	1463	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	81.1265	732	1463	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	81.1179	673	1463	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	81.0854	631	1463	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	81.0108	708	1463	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	80.9929	622	1463	95	below_threshold
Microvirga flavescens	strain=c27j1	GCA_003290125.1	2249811	2249811	type	True	80.9669	637	1463	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	80.811	638	1463	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	80.5946	661	1463	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.1461	364	1463	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.0373	354	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:28,963] [INFO] DFAST Taxonomy check result was written to GCF_015694465.1_ASM1569446v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:28,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:28,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:28,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference/checkm_data
[2024-01-24 12:45:28,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:29,011] [INFO] Task started: CheckM
[2024-01-24 12:45:29,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015694465.1_ASM1569446v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015694465.1_ASM1569446v1_genomic.fna/checkm_input GCF_015694465.1_ASM1569446v1_genomic.fna/checkm_result
[2024-01-24 12:46:09,026] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:09,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:09,054] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:09,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:09,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015694465.1_ASM1569446v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:09,055] [INFO] Task started: Blastn
[2024-01-24 12:46:09,055] [INFO] Running command: blastn -query GCF_015694465.1_ASM1569446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82c0466a-755c-48dc-bbbb-0ed2ff5fc000/dqc_reference/reference_markers_gtdb.fasta -out GCF_015694465.1_ASM1569446v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:11,049] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:11,054] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:11,055] [INFO] Target genome list was writen to GCF_015694465.1_ASM1569446v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:11,069] [INFO] Task started: fastANI
[2024-01-24 12:46:11,069] [INFO] Running command: fastANI --query /var/lib/cwl/stge742ba1e-5826-46a3-9dd1-9a32d7f1448d/GCF_015694465.1_ASM1569446v1_genomic.fna.gz --refList GCF_015694465.1_ASM1569446v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015694465.1_ASM1569446v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:27,384] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:27,400] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:27,400] [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_015694465.1	s__Microvirga sp015694465	100.0	1461	1463	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_011777495.1	s__Microvirga sp011777495	83.8551	877	1463	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	81.4981	667	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013520865.1	s__Microvirga mediterraneensis	81.2219	704	1463	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	81.1736	749	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	81.1708	723	1463	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	81.112	701	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332305.1	s__Microvirga aerophila	81.0733	631	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
GCF_009910705.1	s__Microvirga sp009910705	81.0432	686	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000262405.1	s__Microvirga lotononidis	81.0108	708	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290125.1	s__Microvirga flavescens	80.9773	636	1463	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	80.881	665	1463	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	80.8264	636	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151255.1	s__Microvirga sp003151255	80.6132	658	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017175.1	s__Microvirga vignae	80.5919	661	1463	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 12:46:27,402] [INFO] GTDB search result was written to GCF_015694465.1_ASM1569446v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:27,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:27,406] [INFO] DFAST_QC result json was written to GCF_015694465.1_ASM1569446v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:27,407] [INFO] DFAST_QC completed!
[2024-01-24 12:46:27,407] [INFO] Total running time: 0h1m34s