[2023-06-29 20:14:23,993] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:14:23,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:14:23,999] [INFO] DQC Reference Directory: /var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference
[2023-06-29 20:14:25,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:14:25,517] [INFO] Task started: Prodigal
[2023-06-29 20:14:25,517] [INFO] Running command: gunzip -c /var/lib/cwl/stg23b44ddc-c00e-4d09-8092-8ec906c5d405/GCA_021838385.1_ASM2183838v1_genomic.fna.gz | prodigal -d GCA_021838385.1_ASM2183838v1_genomic.fna/cds.fna -a GCA_021838385.1_ASM2183838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:14:30,035] [INFO] Task succeeded: Prodigal
[2023-06-29 20:14:30,036] [INFO] Task started: HMMsearch
[2023-06-29 20:14:30,036] [INFO] Running command: hmmsearch --tblout GCA_021838385.1_ASM2183838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference/reference_markers.hmm GCA_021838385.1_ASM2183838v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:14:30,239] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:14:30,240] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg23b44ddc-c00e-4d09-8092-8ec906c5d405/GCA_021838385.1_ASM2183838v1_genomic.fna.gz]
[2023-06-29 20:14:30,262] [INFO] Query marker FASTA was written to GCA_021838385.1_ASM2183838v1_genomic.fna/markers.fasta
[2023-06-29 20:14:30,262] [INFO] Task started: Blastn
[2023-06-29 20:14:30,263] [INFO] Running command: blastn -query GCA_021838385.1_ASM2183838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference/reference_markers.fasta -out GCA_021838385.1_ASM2183838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:31,135] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:31,140] [INFO] Selected 17 target genomes.
[2023-06-29 20:14:31,140] [INFO] Target genome list was writen to GCA_021838385.1_ASM2183838v1_genomic.fna/target_genomes.txt
[2023-06-29 20:14:31,141] [INFO] Task started: fastANI
[2023-06-29 20:14:31,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b44ddc-c00e-4d09-8092-8ec906c5d405/GCA_021838385.1_ASM2183838v1_genomic.fna.gz --refList GCA_021838385.1_ASM2183838v1_genomic.fna/target_genomes.txt --output GCA_021838385.1_ASM2183838v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:45,752] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:45,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:45,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:45,769] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:45,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:14:45,770] [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
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	79.0088	163	429	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	79.0083	156	429	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	78.8096	239	429	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.5879	150	429	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	78.0824	216	429	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.4235	198	429	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.335	142	429	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.2766	203	429	95	below_threshold
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	77.2069	126	429	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	77.1969	148	429	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.1649	199	429	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	77.0149	142	429	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.9774	180	429	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	76.9381	154	429	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.9323	147	429	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	76.7782	174	429	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.5807	158	429	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:14:45,777] [INFO] DFAST Taxonomy check result was written to GCA_021838385.1_ASM2183838v1_genomic.fna/tc_result.tsv
[2023-06-29 20:14:45,778] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:45,778] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:45,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference/checkm_data
[2023-06-29 20:14:45,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:45,852] [INFO] Task started: CheckM
[2023-06-29 20:14:45,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021838385.1_ASM2183838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021838385.1_ASM2183838v1_genomic.fna/checkm_input GCA_021838385.1_ASM2183838v1_genomic.fna/checkm_result
[2023-06-29 20:15:05,683] [INFO] Task succeeded: CheckM
[2023-06-29 20:15:05,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:15:05,705] [INFO] ===== Completeness check finished =====
[2023-06-29 20:15:05,706] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:15:05,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021838385.1_ASM2183838v1_genomic.fna/markers.fasta)
[2023-06-29 20:15:05,707] [INFO] Task started: Blastn
[2023-06-29 20:15:05,707] [INFO] Running command: blastn -query GCA_021838385.1_ASM2183838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged5a1e83-0bc1-4d93-9925-3fa2e75392e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_021838385.1_ASM2183838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:15:07,094] [INFO] Task succeeded: Blastn
[2023-06-29 20:15:07,099] [INFO] Selected 19 target genomes.
[2023-06-29 20:15:07,099] [INFO] Target genome list was writen to GCA_021838385.1_ASM2183838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:15:07,100] [INFO] Task started: fastANI
[2023-06-29 20:15:07,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b44ddc-c00e-4d09-8092-8ec906c5d405/GCA_021838385.1_ASM2183838v1_genomic.fna.gz --refList GCA_021838385.1_ASM2183838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021838385.1_ASM2183838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:15:22,246] [INFO] Task succeeded: fastANI
[2023-06-29 20:15:22,268] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:15:22,268] [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
GCA_003133265.1	s__PALSA-911 sp003133265	79.2701	219	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151425.1	s__Palsa-883 sp003151425	79.0906	268	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Palsa-883	95.0	99.82	99.82	0.94	0.94	2	-
GCA_018971455.1	s__REEB85 sp018971455	79.003	147	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	78.8884	269	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCF_002937115.1	s__Rhodopila globiformis	78.7854	241	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	78.748	252	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898425.1	s__69-11 sp001898425	78.743	261	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCA_017307285.1	s__JAFKFI01 sp017307285	78.6345	207	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	78.52	153	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907955.1	s__BOG-930 sp903907955	78.4092	209	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCA_903918195.1	s__BOG-930 sp903918195	78.2555	191	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_008630155.1	s__Rhodovastum atsumiense	78.1137	214	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307335.1	s__JAFKFJ01 sp017307335	77.9993	197	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.9585	201	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	77.756	240	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	77.3513	202	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	77.3025	202	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_018129065.1	s__Roseomonas_B soli	77.2721	187	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896535.1	s__CAITYE01 sp903896535	76.6165	129	429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAITYE01	95.0	99.30	99.07	0.87	0.85	4	-
--------------------------------------------------------------------------------
[2023-06-29 20:15:22,271] [INFO] GTDB search result was written to GCA_021838385.1_ASM2183838v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:15:22,272] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:15:22,280] [INFO] DFAST_QC result json was written to GCA_021838385.1_ASM2183838v1_genomic.fna/dqc_result.json
[2023-06-29 20:15:22,280] [INFO] DFAST_QC completed!
[2023-06-29 20:15:22,280] [INFO] Total running time: 0h0m58s