[2024-01-24 13:33:11,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:11,202] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:11,202] [INFO] DQC Reference Directory: /var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference
[2024-01-24 13:33:12,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,625] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg3461dd6f-e657-43db-ab7e-00da53220018/GCF_000021745.1_ASM2174v1_genomic.fna.gz | prodigal -d GCF_000021745.1_ASM2174v1_genomic.fna/cds.fna -a GCF_000021745.1_ASM2174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:25,300] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:25,300] [INFO] Task started: HMMsearch
[2024-01-24 13:33:25,300] [INFO] Running command: hmmsearch --tblout GCF_000021745.1_ASM2174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference/reference_markers.hmm GCF_000021745.1_ASM2174v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:25,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:25,591] [INFO] Found 6/6 markers.
[2024-01-24 13:33:25,630] [INFO] Query marker FASTA was written to GCF_000021745.1_ASM2174v1_genomic.fna/markers.fasta
[2024-01-24 13:33:25,631] [INFO] Task started: Blastn
[2024-01-24 13:33:25,631] [INFO] Running command: blastn -query GCF_000021745.1_ASM2174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference/reference_markers.fasta -out GCF_000021745.1_ASM2174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:26,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:26,688] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:26,688] [INFO] Target genome list was writen to GCF_000021745.1_ASM2174v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:26,697] [INFO] Task started: fastANI
[2024-01-24 13:33:26,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg3461dd6f-e657-43db-ab7e-00da53220018/GCF_000021745.1_ASM2174v1_genomic.fna.gz --refList GCF_000021745.1_ASM2174v1_genomic.fna/target_genomes.txt --output GCF_000021745.1_ASM2174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:43,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:43,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:43,679] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:43,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:43,679] [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
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	100.0	1434	1435	95	conclusive
Methylocapsa acidiphila	strain=B2	GCA_000427445.1	133552	133552	type	True	78.5214	432	1435	95	below_threshold
Methylocapsa aurea	strain=KYG	GCA_000746085.1	663610	663610	type	True	78.5111	458	1435	95	below_threshold
Methylocapsa palsarum	strain=NE2	GCA_900114285.1	1612308	1612308	type	True	78.4512	394	1435	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_004135935.1	569860	569860	type	True	78.0714	327	1435	95	below_threshold
Methylovirgula ligni	strain=BW863	GCA_003387225.1	569860	569860	type	True	78.0022	328	1435	95	below_threshold
Methyloferula stellata	strain=AR4T	GCA_000385335.1	876270	876270	type	True	77.9361	332	1435	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	77.8432	396	1435	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.773	303	1435	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	77.6602	256	1435	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	77.5635	259	1435	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	77.5534	269	1435	95	below_threshold
Beijerinckia indica subsp. indica	strain=ATCC 9039	GCA_000019845.1	31994	533	type	True	77.5229	256	1435	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	77.4287	351	1435	95	below_threshold
Beijerinckia mobilis	strain=UQM 1969	GCA_000745425.1	231434	231434	type	True	77.4159	264	1435	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	77.402	339	1435	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	76.9277	286	1435	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.8352	254	1435	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.8094	264	1435	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.4928	230	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,681] [INFO] DFAST Taxonomy check result was written to GCF_000021745.1_ASM2174v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:43,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:43,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:43,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference/checkm_data
[2024-01-24 13:33:43,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:43,728] [INFO] Task started: CheckM
[2024-01-24 13:33:43,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021745.1_ASM2174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021745.1_ASM2174v1_genomic.fna/checkm_input GCF_000021745.1_ASM2174v1_genomic.fna/checkm_result
[2024-01-24 13:34:20,419] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:20,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:20,443] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:20,443] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:20,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021745.1_ASM2174v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:20,444] [INFO] Task started: Blastn
[2024-01-24 13:34:20,445] [INFO] Running command: blastn -query GCF_000021745.1_ASM2174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff5d613a-056d-4753-928f-fd7b27ee00dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021745.1_ASM2174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:22,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:22,369] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:22,369] [INFO] Target genome list was writen to GCF_000021745.1_ASM2174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:22,395] [INFO] Task started: fastANI
[2024-01-24 13:34:22,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg3461dd6f-e657-43db-ab7e-00da53220018/GCF_000021745.1_ASM2174v1_genomic.fna.gz --refList GCF_000021745.1_ASM2174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021745.1_ASM2174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:32,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:32,063] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:32,064] [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_000021745.1	s__Methylocella silvestris	100.0	1435	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002891535.1	s__Methylocella silvestris_A	90.6991	1158	1435	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	79.7681	688	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	97.31	97.31	0.88	0.88	2	-
GCF_000427445.1	s__Methylocella acidiphila	78.5274	432	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746085.1	s__Methylocella aurea	78.4893	461	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114285.1	s__Methylocella palsarum	78.451	394	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135935.1	s__Methylovirgula ligni	78.0825	326	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylovirgula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015709515.1	s__Methylocystis sp015709515	77.6334	282	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745215.1	s__Methylosinus sp000745215	77.5989	361	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773555.1	s__Methylocystis sp009773555	77.5898	247	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.69	99.47	0.95	0.93	3	-
GCF_009765775.1	s__RH-AL1 sp009765775	77.5011	317	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:32,066] [INFO] GTDB search result was written to GCF_000021745.1_ASM2174v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:32,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:32,071] [INFO] DFAST_QC result json was written to GCF_000021745.1_ASM2174v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:32,071] [INFO] DFAST_QC completed!
[2024-01-24 13:34:32,071] [INFO] Total running time: 0h1m21s