[2024-01-24 14:05:31,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,238] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference
[2024-01-24 14:05:32,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,440] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,441] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa7d85a5-3375-4b69-bd11-c82d03aa59ed/GCF_000019845.1_ASM1984v1_genomic.fna.gz | prodigal -d GCF_000019845.1_ASM1984v1_genomic.fna/cds.fna -a GCF_000019845.1_ASM1984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:45,841] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:45,841] [INFO] Task started: HMMsearch
[2024-01-24 14:05:45,841] [INFO] Running command: hmmsearch --tblout GCF_000019845.1_ASM1984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference/reference_markers.hmm GCF_000019845.1_ASM1984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:46,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:46,132] [INFO] Found 6/6 markers.
[2024-01-24 14:05:46,170] [INFO] Query marker FASTA was written to GCF_000019845.1_ASM1984v1_genomic.fna/markers.fasta
[2024-01-24 14:05:46,170] [INFO] Task started: Blastn
[2024-01-24 14:05:46,170] [INFO] Running command: blastn -query GCF_000019845.1_ASM1984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference/reference_markers.fasta -out GCF_000019845.1_ASM1984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:46,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:46,955] [INFO] Selected 16 target genomes.
[2024-01-24 14:05:46,956] [INFO] Target genome list was writen to GCF_000019845.1_ASM1984v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:46,963] [INFO] Task started: fastANI
[2024-01-24 14:05:46,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa7d85a5-3375-4b69-bd11-c82d03aa59ed/GCF_000019845.1_ASM1984v1_genomic.fna.gz --refList GCF_000019845.1_ASM1984v1_genomic.fna/target_genomes.txt --output GCF_000019845.1_ASM1984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:00,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:00,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:00,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:00,293] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:00,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:00,294] [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
Beijerinckia indica subsp. indica	strain=ATCC 9039	GCA_000019845.1	31994	533	type	True	100.0	1472	1472	95	conclusive
Beijerinckia mobilis	strain=UQM 1969	GCA_000745425.1	231434	231434	type	True	79.7978	619	1472	95	below_threshold
Methyloferula stellata	strain=AR4T	GCA_000385335.1	876270	876270	type	True	77.8026	264	1472	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	77.6997	248	1472	95	below_threshold
Methylocapsa acidiphila	strain=B2	GCA_000427445.1	133552	133552	type	True	77.6414	244	1472	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.5262	167	1472	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_004135935.1	569860	569860	type	True	77.4771	201	1472	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_003387225.1	569860	569860	type	True	77.4676	194	1472	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	77.2017	189	1472	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.1319	99	1472	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	76.8177	137	1472	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.646	111	1472	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	76.5368	120	1472	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.4439	84	1472	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	75.989	74	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:00,295] [INFO] DFAST Taxonomy check result was written to GCF_000019845.1_ASM1984v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:00,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:00,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:00,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference/checkm_data
[2024-01-24 14:06:00,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:00,347] [INFO] Task started: CheckM
[2024-01-24 14:06:00,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000019845.1_ASM1984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000019845.1_ASM1984v1_genomic.fna/checkm_input GCF_000019845.1_ASM1984v1_genomic.fna/checkm_result
[2024-01-24 14:06:45,315] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:45,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:45,356] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:45,357] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:45,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000019845.1_ASM1984v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:45,358] [INFO] Task started: Blastn
[2024-01-24 14:06:45,358] [INFO] Running command: blastn -query GCF_000019845.1_ASM1984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7720ea5-d22b-4b17-a1ba-8ea6983ac95f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000019845.1_ASM1984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,841] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,845] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:46,846] [INFO] Target genome list was writen to GCF_000019845.1_ASM1984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:46,869] [INFO] Task started: fastANI
[2024-01-24 14:06:46,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa7d85a5-3375-4b69-bd11-c82d03aa59ed/GCF_000019845.1_ASM1984v1_genomic.fna.gz --refList GCF_000019845.1_ASM1984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000019845.1_ASM1984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:00,473] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:00,491] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:00,492] [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_000019845.1	s__Beijerinckia indica	100.0	1472	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Beijerinckia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000745425.1	s__Beijerinckia mobilis	79.7842	621	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Beijerinckia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385335.1	s__Methyloferula stellata	77.8026	264	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021745.1	s__Methylocella silvestris	77.7052	247	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427445.1	s__Methylocella acidiphila	77.6972	246	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891535.1	s__Methylocella silvestris_A	77.6194	229	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901905185.1	s__Methylocella tundrae	77.4889	235	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	97.31	97.31	0.88	0.88	2	-
GCF_004135935.1	s__Methylovirgula ligni	77.4771	201	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylovirgula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902506165.1	s__Bosea sp902506165	76.8606	130	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.97	1.00	1.00	8	-
GCF_900156025.1	s__Bosea sp900156025	76.8272	125	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.08	99.08	0.82	0.82	2	-
GCA_903861645.1	s__28-YEA-48 sp903861645	76.8121	139	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	99.51	98.79	0.96	0.94	5	-
GCF_003722355.1	s__Methylocystis hirsuta	76.774	135	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.95	95.95	0.95	0.95	2	-
GCA_003105285.1	s__Methylosinus sp003105285	76.6771	136	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655535.1	s__Methyloferula sp015655535	76.6722	174	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898965.1	s__28-YEA-48 sp001898965	76.6032	163	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005771425.1	s__Methylocystis sp005771425	76.5418	116	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930675.1	s__CAIYZJ01 sp903930675	76.3948	79	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	97.85	97.85	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,494] [INFO] GTDB search result was written to GCF_000019845.1_ASM1984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:00,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:00,498] [INFO] DFAST_QC result json was written to GCF_000019845.1_ASM1984v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:00,498] [INFO] DFAST_QC completed!
[2024-01-24 14:07:00,498] [INFO] Total running time: 0h1m29s