[2024-01-24 12:30:48,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,279] [INFO] DQC Reference Directory: /var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference
[2024-01-24 12:30:49,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:49,473] [INFO] Task started: Prodigal
[2024-01-24 12:30:49,473] [INFO] Running command: gunzip -c /var/lib/cwl/stgce2ab73b-13c1-450e-b077-42a4a594f221/GCF_020532555.1_ASM2053255v1_genomic.fna.gz | prodigal -d GCF_020532555.1_ASM2053255v1_genomic.fna/cds.fna -a GCF_020532555.1_ASM2053255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:01,999] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:02,000] [INFO] Task started: HMMsearch
[2024-01-24 12:31:02,000] [INFO] Running command: hmmsearch --tblout GCF_020532555.1_ASM2053255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference/reference_markers.hmm GCF_020532555.1_ASM2053255v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:02,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:02,237] [INFO] Found 6/6 markers.
[2024-01-24 12:31:02,275] [INFO] Query marker FASTA was written to GCF_020532555.1_ASM2053255v1_genomic.fna/markers.fasta
[2024-01-24 12:31:02,275] [INFO] Task started: Blastn
[2024-01-24 12:31:02,275] [INFO] Running command: blastn -query GCF_020532555.1_ASM2053255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference/reference_markers.fasta -out GCF_020532555.1_ASM2053255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,292] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,295] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:03,295] [INFO] Target genome list was writen to GCF_020532555.1_ASM2053255v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:03,310] [INFO] Task started: fastANI
[2024-01-24 12:31:03,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgce2ab73b-13c1-450e-b077-42a4a594f221/GCF_020532555.1_ASM2053255v1_genomic.fna.gz --refList GCF_020532555.1_ASM2053255v1_genomic.fna/target_genomes.txt --output GCF_020532555.1_ASM2053255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:19,048] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:19,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:19,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:19,061] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:19,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:19,062] [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 lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	100.0	1484	1485	95	conclusive
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	84.6488	1012	1485	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	83.0179	897	1485	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	82.837	777	1485	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.7961	874	1485	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	82.6555	844	1485	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	82.5418	848	1485	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	82.4749	861	1485	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	82.4539	844	1485	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	82.3247	863	1485	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	81.9172	815	1485	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.6652	520	1485	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.6559	545	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:19,063] [INFO] DFAST Taxonomy check result was written to GCF_020532555.1_ASM2053255v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:19,064] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:19,064] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:19,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference/checkm_data
[2024-01-24 12:31:19,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:19,118] [INFO] Task started: CheckM
[2024-01-24 12:31:19,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020532555.1_ASM2053255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020532555.1_ASM2053255v1_genomic.fna/checkm_input GCF_020532555.1_ASM2053255v1_genomic.fna/checkm_result
[2024-01-24 12:31:58,732] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:58,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:58,755] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:58,755] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:58,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020532555.1_ASM2053255v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:58,756] [INFO] Task started: Blastn
[2024-01-24 12:31:58,756] [INFO] Running command: blastn -query GCF_020532555.1_ASM2053255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda26b161-1415-4182-a4d3-88a85b5828e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_020532555.1_ASM2053255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:00,738] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:00,741] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:00,741] [INFO] Target genome list was writen to GCF_020532555.1_ASM2053255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:00,751] [INFO] Task started: fastANI
[2024-01-24 12:32:00,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgce2ab73b-13c1-450e-b077-42a4a594f221/GCF_020532555.1_ASM2053255v1_genomic.fna.gz --refList GCF_020532555.1_ASM2053255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020532555.1_ASM2053255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:19,054] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:19,067] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:32:19,068] [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_003350535.1	s__Microvirga subterranea	84.6488	1012	1485	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	83.0211	852	1485	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	83.0044	898	1485	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	82.8423	776	1485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003332305.1	s__Microvirga aerophila	82.6526	845	1485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
GCF_013520865.1	s__Microvirga mediterraneensis	82.6131	850	1485	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	82.4881	860	1485	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	82.4633	843	1485	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	82.4379	879	1485	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	82.4053	841	1485	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	82.376	861	1485	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	82.3567	830	1485	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	82.3305	863	1485	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	82.3013	910	1485	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	82.2927	844	1485	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	81.9374	813	1485	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 12:32:19,069] [INFO] GTDB search result was written to GCF_020532555.1_ASM2053255v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:19,070] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:19,073] [INFO] DFAST_QC result json was written to GCF_020532555.1_ASM2053255v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:19,074] [INFO] DFAST_QC completed!
[2024-01-24 12:32:19,074] [INFO] Total running time: 0h1m31s