[2023-06-29 15:55:05,958] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:55:05,961] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:55:05,962] [INFO] DQC Reference Directory: /var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference
[2023-06-29 15:55:07,437] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:55:07,438] [INFO] Task started: Prodigal
[2023-06-29 15:55:07,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f4f5c03-8b8e-4e19-8234-c44a51efa285/GCA_021778095.1_ASM2177809v1_genomic.fna.gz | prodigal -d GCA_021778095.1_ASM2177809v1_genomic.fna/cds.fna -a GCA_021778095.1_ASM2177809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:55:11,338] [INFO] Task succeeded: Prodigal
[2023-06-29 15:55:11,339] [INFO] Task started: HMMsearch
[2023-06-29 15:55:11,339] [INFO] Running command: hmmsearch --tblout GCA_021778095.1_ASM2177809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference/reference_markers.hmm GCA_021778095.1_ASM2177809v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:55:11,535] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:55:11,536] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8f4f5c03-8b8e-4e19-8234-c44a51efa285/GCA_021778095.1_ASM2177809v1_genomic.fna.gz]
[2023-06-29 15:55:11,557] [INFO] Query marker FASTA was written to GCA_021778095.1_ASM2177809v1_genomic.fna/markers.fasta
[2023-06-29 15:55:11,558] [INFO] Task started: Blastn
[2023-06-29 15:55:11,558] [INFO] Running command: blastn -query GCA_021778095.1_ASM2177809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference/reference_markers.fasta -out GCA_021778095.1_ASM2177809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:55:12,400] [INFO] Task succeeded: Blastn
[2023-06-29 15:55:12,404] [INFO] Selected 22 target genomes.
[2023-06-29 15:55:12,405] [INFO] Target genome list was writen to GCA_021778095.1_ASM2177809v1_genomic.fna/target_genomes.txt
[2023-06-29 15:55:12,408] [INFO] Task started: fastANI
[2023-06-29 15:55:12,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4f5c03-8b8e-4e19-8234-c44a51efa285/GCA_021778095.1_ASM2177809v1_genomic.fna.gz --refList GCA_021778095.1_ASM2177809v1_genomic.fna/target_genomes.txt --output GCA_021778095.1_ASM2177809v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:55:28,543] [INFO] Task succeeded: fastANI
[2023-06-29 15:55:28,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:55:28,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:55:28,563] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:55:28,563] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:55:28,564] [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_000964345.1	62140	62140	type	True	77.5627	162	395	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.533	124	395	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.4687	186	395	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.4358	174	395	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	77.0735	118	395	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	77.0511	119	395	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.0445	120	395	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.0344	148	395	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.8873	180	395	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.8632	152	395	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	76.8079	146	395	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.7446	148	395	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.7016	164	395	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.6879	122	395	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.6276	107	395	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.56	112	395	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	76.5429	121	395	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.5374	119	395	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	76.4561	80	395	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	76.4133	81	395	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	76.3955	76	395	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	75.9002	150	395	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:55:28,566] [INFO] DFAST Taxonomy check result was written to GCA_021778095.1_ASM2177809v1_genomic.fna/tc_result.tsv
[2023-06-29 15:55:28,567] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:55:28,567] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:55:28,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference/checkm_data
[2023-06-29 15:55:28,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:55:28,591] [INFO] Task started: CheckM
[2023-06-29 15:55:28,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021778095.1_ASM2177809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021778095.1_ASM2177809v1_genomic.fna/checkm_input GCA_021778095.1_ASM2177809v1_genomic.fna/checkm_result
[2023-06-29 15:55:46,768] [INFO] Task succeeded: CheckM
[2023-06-29 15:55:46,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:55:46,806] [INFO] ===== Completeness check finished =====
[2023-06-29 15:55:46,806] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:55:46,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021778095.1_ASM2177809v1_genomic.fna/markers.fasta)
[2023-06-29 15:55:46,807] [INFO] Task started: Blastn
[2023-06-29 15:55:46,807] [INFO] Running command: blastn -query GCA_021778095.1_ASM2177809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge10c7f9b-e148-46ae-84d2-9d4693143845/dqc_reference/reference_markers_gtdb.fasta -out GCA_021778095.1_ASM2177809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:55:48,290] [INFO] Task succeeded: Blastn
[2023-06-29 15:55:48,295] [INFO] Selected 19 target genomes.
[2023-06-29 15:55:48,295] [INFO] Target genome list was writen to GCA_021778095.1_ASM2177809v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:55:48,307] [INFO] Task started: fastANI
[2023-06-29 15:55:48,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4f5c03-8b8e-4e19-8234-c44a51efa285/GCA_021778095.1_ASM2177809v1_genomic.fna.gz --refList GCA_021778095.1_ASM2177809v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021778095.1_ASM2177809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:56:02,078] [INFO] Task succeeded: fastANI
[2023-06-29 15:56:02,097] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:56:02,097] [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_018971455.1	s__REEB85 sp018971455	78.1231	124	395	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	77.8169	202	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.764	168	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	77.6146	164	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	77.5337	162	395	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	77.5093	125	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	77.4472	175	395	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_903907955.1	s__BOG-930 sp903907955	77.3645	155	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCF_014644455.1	s__Caldovatus sediminis	77.2719	194	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	77.2135	153	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCA_003133265.1	s__PALSA-911 sp003133265	77.115	135	395	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_017307335.1	s__JAFKFJ01 sp017307335	77.0791	164	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937115.1	s__Rhodopila globiformis	77.0175	149	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	76.8739	128	395	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_007129145.1	s__Roseococcus sp007129145	76.8324	87	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944925.1	s__Rhodopila sp903944925	76.7605	118	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
GCF_018129085.1	s__Roseomonas_C hellenica	76.742	161	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	97.71	97.71	0.92	0.92	2	-
GCF_017355885.1	s__Roseococcus sp017355885	76.675	103	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805645.1	s__CADCTG01 sp902805645	76.4096	114	395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CADCTG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:56:02,099] [INFO] GTDB search result was written to GCA_021778095.1_ASM2177809v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:56:02,100] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:56:02,105] [INFO] DFAST_QC result json was written to GCA_021778095.1_ASM2177809v1_genomic.fna/dqc_result.json
[2023-06-29 15:56:02,105] [INFO] DFAST_QC completed!
[2023-06-29 15:56:02,105] [INFO] Total running time: 0h0m56s