[2023-06-29 08:24:17,995] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:24:17,997] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:24:17,998] [INFO] DQC Reference Directory: /var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference
[2023-06-29 08:24:20,051] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:24:20,052] [INFO] Task started: Prodigal
[2023-06-29 08:24:20,053] [INFO] Running command: gunzip -c /var/lib/cwl/stg76219622-6349-4afc-8e39-29bcb0b70358/GCA_027433975.1_ASM2743397v1_genomic.fna.gz | prodigal -d GCA_027433975.1_ASM2743397v1_genomic.fna/cds.fna -a GCA_027433975.1_ASM2743397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:24:27,496] [INFO] Task succeeded: Prodigal
[2023-06-29 08:24:27,496] [INFO] Task started: HMMsearch
[2023-06-29 08:24:27,496] [INFO] Running command: hmmsearch --tblout GCA_027433975.1_ASM2743397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference/reference_markers.hmm GCA_027433975.1_ASM2743397v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:24:27,751] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:24:27,752] [INFO] Found 6/6 markers.
[2023-06-29 08:24:27,783] [INFO] Query marker FASTA was written to GCA_027433975.1_ASM2743397v1_genomic.fna/markers.fasta
[2023-06-29 08:24:27,783] [INFO] Task started: Blastn
[2023-06-29 08:24:27,783] [INFO] Running command: blastn -query GCA_027433975.1_ASM2743397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference/reference_markers.fasta -out GCA_027433975.1_ASM2743397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:24:28,644] [INFO] Task succeeded: Blastn
[2023-06-29 08:24:28,661] [INFO] Selected 21 target genomes.
[2023-06-29 08:24:28,662] [INFO] Target genome list was writen to GCA_027433975.1_ASM2743397v1_genomic.fna/target_genomes.txt
[2023-06-29 08:24:28,667] [INFO] Task started: fastANI
[2023-06-29 08:24:28,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg76219622-6349-4afc-8e39-29bcb0b70358/GCA_027433975.1_ASM2743397v1_genomic.fna.gz --refList GCA_027433975.1_ASM2743397v1_genomic.fna/target_genomes.txt --output GCA_027433975.1_ASM2743397v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:24:43,460] [INFO] Task succeeded: fastANI
[2023-06-29 08:24:43,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:24:43,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:24:43,478] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:24:43,478] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:24:43,478] [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
Acidocella aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	79.2238	377	782	95	below_threshold
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	78.7041	357	782	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.6139	201	782	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.509	224	782	95	below_threshold
Acidocella aminolytica	strain=DSM 11237	GCA_900129125.1	33998	33998	type	True	77.4923	238	782	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.2565	177	782	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.8076	184	782	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	76.7899	159	782	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.6149	165	782	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	76.598	119	782	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.5844	130	782	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.5598	165	782	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.5469	178	782	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	76.5373	157	782	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.4165	174	782	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	76.3964	72	782	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	76.3336	87	782	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	76.3229	170	782	95	below_threshold
Komagataeibacter rhaeticus	strain=LMG 22126	GCA_003207855.1	215221	215221	type	True	76.1685	94	782	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.9132	117	782	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	75.545	75	782	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:24:43,481] [INFO] DFAST Taxonomy check result was written to GCA_027433975.1_ASM2743397v1_genomic.fna/tc_result.tsv
[2023-06-29 08:24:43,481] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:24:43,481] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:24:43,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference/checkm_data
[2023-06-29 08:24:43,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:24:43,518] [INFO] Task started: CheckM
[2023-06-29 08:24:43,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027433975.1_ASM2743397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027433975.1_ASM2743397v1_genomic.fna/checkm_input GCA_027433975.1_ASM2743397v1_genomic.fna/checkm_result
[2023-06-29 08:25:10,297] [INFO] Task succeeded: CheckM
[2023-06-29 08:25:10,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 08:25:10,322] [INFO] ===== Completeness check finished =====
[2023-06-29 08:25:10,323] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:25:10,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027433975.1_ASM2743397v1_genomic.fna/markers.fasta)
[2023-06-29 08:25:10,324] [INFO] Task started: Blastn
[2023-06-29 08:25:10,324] [INFO] Running command: blastn -query GCA_027433975.1_ASM2743397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3fb9814-d6b0-43b5-aaeb-b0b8fce005a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_027433975.1_ASM2743397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:25:11,800] [INFO] Task succeeded: Blastn
[2023-06-29 08:25:11,805] [INFO] Selected 11 target genomes.
[2023-06-29 08:25:11,805] [INFO] Target genome list was writen to GCA_027433975.1_ASM2743397v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:25:11,813] [INFO] Task started: fastANI
[2023-06-29 08:25:11,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg76219622-6349-4afc-8e39-29bcb0b70358/GCA_027433975.1_ASM2743397v1_genomic.fna.gz --refList GCA_027433975.1_ASM2743397v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027433975.1_ASM2743397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:25:18,411] [INFO] Task succeeded: fastANI
[2023-06-29 08:25:18,424] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:25:18,424] [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_013044125.1	s__Acidocella sp013044125	94.3098	608	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164135.1	s__Acidocella sp003164135	84.0803	549	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.77	99.73	0.97	0.95	5	-
GCF_014201825.1	s__Acidocella aromatica	79.2355	376	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687875.1	s__Acidocella facilis	78.7104	357	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
GCA_018971725.1	s__Acidocella sp018971725	78.299	216	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971565.1	s__Acidocella sp018971565	78.2559	207	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255575.1	s__Acidocella sp002255575	77.6091	204	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.72	99.72	0.92	0.92	2	-
GCA_003137135.1	s__Acidocella sp003137135	77.5543	233	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.49	99.49	0.84	0.84	2	-
GCF_000164635.1	s__Roseomonas cervicalis	76.7699	187	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005844085.1	s__Lichenicoccus roseus	76.7639	139	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240635.1	s__JAFAYA01 sp019240635	76.2977	119	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:25:18,426] [INFO] GTDB search result was written to GCA_027433975.1_ASM2743397v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:25:18,426] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:25:18,430] [INFO] DFAST_QC result json was written to GCA_027433975.1_ASM2743397v1_genomic.fna/dqc_result.json
[2023-06-29 08:25:18,430] [INFO] DFAST_QC completed!
[2023-06-29 08:25:18,430] [INFO] Total running time: 0h1m0s