[2023-06-19 01:46:29,510] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:46:29,512] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:46:29,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference
[2023-06-19 01:46:30,717] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:46:30,718] [INFO] Task started: Prodigal
[2023-06-19 01:46:30,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg092d6d2f-d4f5-45e5-8449-cd1c17852eac/GCA_018401385.1_ASM1840138v1_genomic.fna.gz | prodigal -d GCA_018401385.1_ASM1840138v1_genomic.fna/cds.fna -a GCA_018401385.1_ASM1840138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:46:37,367] [INFO] Task succeeded: Prodigal
[2023-06-19 01:46:37,367] [INFO] Task started: HMMsearch
[2023-06-19 01:46:37,367] [INFO] Running command: hmmsearch --tblout GCA_018401385.1_ASM1840138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference/reference_markers.hmm GCA_018401385.1_ASM1840138v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:46:37,529] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:46:37,530] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg092d6d2f-d4f5-45e5-8449-cd1c17852eac/GCA_018401385.1_ASM1840138v1_genomic.fna.gz]
[2023-06-19 01:46:37,553] [INFO] Query marker FASTA was written to GCA_018401385.1_ASM1840138v1_genomic.fna/markers.fasta
[2023-06-19 01:46:37,553] [INFO] Task started: Blastn
[2023-06-19 01:46:37,553] [INFO] Running command: blastn -query GCA_018401385.1_ASM1840138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference/reference_markers.fasta -out GCA_018401385.1_ASM1840138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:38,153] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:38,159] [INFO] Selected 23 target genomes.
[2023-06-19 01:46:38,159] [INFO] Target genome list was writen to GCA_018401385.1_ASM1840138v1_genomic.fna/target_genomes.txt
[2023-06-19 01:46:38,160] [INFO] Task started: fastANI
[2023-06-19 01:46:38,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg092d6d2f-d4f5-45e5-8449-cd1c17852eac/GCA_018401385.1_ASM1840138v1_genomic.fna.gz --refList GCA_018401385.1_ASM1840138v1_genomic.fna/target_genomes.txt --output GCA_018401385.1_ASM1840138v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:46:52,021] [INFO] Task succeeded: fastANI
[2023-06-19 01:46:52,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:46:52,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:46:52,039] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:46:52,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:46:52,039] [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
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.8694	96	603	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	76.8499	99	603	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.8002	87	603	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.7984	112	603	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.7261	81	603	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.5608	57	603	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.5297	57	603	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.4495	73	603	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	76.3719	70	603	95	below_threshold
Roseinatronobacter monicus	strain=DSM 18423	GCA_006716865.1	393481	393481	type	True	76.3674	85	603	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	76.3644	69	603	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3369	64	603	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.3368	58	603	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3089	65	603	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	76.2394	57	603	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.2316	79	603	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	76.2125	64	603	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	76.212	57	603	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.1962	82	603	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	76.1767	69	603	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.0823	59	603	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	75.8156	71	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:46:52,041] [INFO] DFAST Taxonomy check result was written to GCA_018401385.1_ASM1840138v1_genomic.fna/tc_result.tsv
[2023-06-19 01:46:52,042] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:46:52,042] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:46:52,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference/checkm_data
[2023-06-19 01:46:52,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:46:52,067] [INFO] Task started: CheckM
[2023-06-19 01:46:52,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018401385.1_ASM1840138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018401385.1_ASM1840138v1_genomic.fna/checkm_input GCA_018401385.1_ASM1840138v1_genomic.fna/checkm_result
[2023-06-19 01:47:16,880] [INFO] Task succeeded: CheckM
[2023-06-19 01:47:16,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:47:16,905] [INFO] ===== Completeness check finished =====
[2023-06-19 01:47:16,905] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:47:16,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018401385.1_ASM1840138v1_genomic.fna/markers.fasta)
[2023-06-19 01:47:16,906] [INFO] Task started: Blastn
[2023-06-19 01:47:16,906] [INFO] Running command: blastn -query GCA_018401385.1_ASM1840138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84dee48a-6faa-4a96-9d07-5deec601bde3/dqc_reference/reference_markers_gtdb.fasta -out GCA_018401385.1_ASM1840138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:47:17,716] [INFO] Task succeeded: Blastn
[2023-06-19 01:47:17,721] [INFO] Selected 13 target genomes.
[2023-06-19 01:47:17,721] [INFO] Target genome list was writen to GCA_018401385.1_ASM1840138v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:47:17,725] [INFO] Task started: fastANI
[2023-06-19 01:47:17,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg092d6d2f-d4f5-45e5-8449-cd1c17852eac/GCA_018401385.1_ASM1840138v1_genomic.fna.gz --refList GCA_018401385.1_ASM1840138v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018401385.1_ASM1840138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:47:25,078] [INFO] Task succeeded: fastANI
[2023-06-19 01:47:25,089] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:47:25,089] [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_018401385.1	s__M30B80 sp018401385	100.0	599	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__M30B80	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015693905.1	s__M30B80 sp015693905	82.5309	470	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__M30B80	95.0	97.47	96.18	0.91	0.87	8	-
GCA_015689775.1	s__M30B80 sp015689775	81.8786	404	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__M30B80	95.0	99.19	99.19	0.96	0.96	2	-
GCA_018402035.1	s__Roseicyclus sp018402035	77.1795	139	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	76.932	112	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689735.1	s__Roseicyclus sp015689735	76.9047	124	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	76.8694	96	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018401965.1	s__Roseicyclus sp018401965	76.8628	121	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	76.7984	112	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	76.7395	72	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	76.7263	91	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688285.1	s__Rhodophyticola porphyridii	76.7261	81	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	76.7	91	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:47:25,091] [INFO] GTDB search result was written to GCA_018401385.1_ASM1840138v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:47:25,092] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:47:25,097] [INFO] DFAST_QC result json was written to GCA_018401385.1_ASM1840138v1_genomic.fna/dqc_result.json
[2023-06-19 01:47:25,097] [INFO] DFAST_QC completed!
[2023-06-19 01:47:25,097] [INFO] Total running time: 0h0m56s