[2024-01-24 13:32:18,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference
[2024-01-24 13:32:19,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,425] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,425] [INFO] Running command: gunzip -c /var/lib/cwl/stgebd89343-2ffb-4aea-b37d-9f54f2ec443d/GCF_018863235.1_ASM1886323v1_genomic.fna.gz | prodigal -d GCF_018863235.1_ASM1886323v1_genomic.fna/cds.fna -a GCF_018863235.1_ASM1886323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:31,379] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:31,379] [INFO] Task started: HMMsearch
[2024-01-24 13:32:31,379] [INFO] Running command: hmmsearch --tblout GCF_018863235.1_ASM1886323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference/reference_markers.hmm GCF_018863235.1_ASM1886323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:31,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:31,661] [INFO] Found 6/6 markers.
[2024-01-24 13:32:31,700] [INFO] Query marker FASTA was written to GCF_018863235.1_ASM1886323v1_genomic.fna/markers.fasta
[2024-01-24 13:32:31,701] [INFO] Task started: Blastn
[2024-01-24 13:32:31,701] [INFO] Running command: blastn -query GCF_018863235.1_ASM1886323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference/reference_markers.fasta -out GCF_018863235.1_ASM1886323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:32,465] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:32,468] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:32,469] [INFO] Target genome list was writen to GCF_018863235.1_ASM1886323v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:32,476] [INFO] Task started: fastANI
[2024-01-24 13:32:32,476] [INFO] Running command: fastANI --query /var/lib/cwl/stgebd89343-2ffb-4aea-b37d-9f54f2ec443d/GCF_018863235.1_ASM1886323v1_genomic.fna.gz --refList GCF_018863235.1_ASM1886323v1_genomic.fna/target_genomes.txt --output GCF_018863235.1_ASM1886323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:48,388] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:48,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:48,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:48,403] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:48,403] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:48,403] [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
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	100.0	1372	1372	95	conclusive
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	79.9401	476	1372	95	below_threshold
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	78.0736	235	1372	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	77.341	183	1372	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	77.3208	103	1372	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	77.2463	104	1372	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	77.1345	110	1372	95	below_threshold
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	76.8611	83	1372	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	76.8003	85	1372	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	76.7999	87	1372	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	76.7724	94	1372	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	76.5269	86	1372	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	76.5052	81	1372	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	76.2818	97	1372	95	below_threshold
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	76.0566	73	1372	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.0344	51	1372	95	below_threshold
Marinibactrum halimedae	strain=NBRC 110095	GCA_021234875.1	1444977	1444977	type	True	75.7432	54	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:48,406] [INFO] DFAST Taxonomy check result was written to GCF_018863235.1_ASM1886323v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:48,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:48,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:48,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference/checkm_data
[2024-01-24 13:32:48,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:48,469] [INFO] Task started: CheckM
[2024-01-24 13:32:48,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018863235.1_ASM1886323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018863235.1_ASM1886323v1_genomic.fna/checkm_input GCF_018863235.1_ASM1886323v1_genomic.fna/checkm_result
[2024-01-24 13:33:29,596] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:29,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:29,612] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:29,612] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:29,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018863235.1_ASM1886323v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:29,613] [INFO] Task started: Blastn
[2024-01-24 13:33:29,613] [INFO] Running command: blastn -query GCF_018863235.1_ASM1886323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2158c0-0c5f-4d1b-acf8-2d94f599bc0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018863235.1_ASM1886323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:30,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:30,860] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:30,861] [INFO] Target genome list was writen to GCF_018863235.1_ASM1886323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:30,882] [INFO] Task started: fastANI
[2024-01-24 13:33:30,882] [INFO] Running command: fastANI --query /var/lib/cwl/stgebd89343-2ffb-4aea-b37d-9f54f2ec443d/GCF_018863235.1_ASM1886323v1_genomic.fna.gz --refList GCF_018863235.1_ASM1886323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018863235.1_ASM1886323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:43,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,392] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:43,393] [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_018863235.1	s__Pseudomaricurvus sp018863235	100.0	1372	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	79.9258	478	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	78.0652	234	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	78.0563	239	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707785.1	s__Pseudomaricurvus sp002707785	77.922	209	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	99.83	99.83	0.94	0.94	2	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	77.341	183	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	77.2925	104	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_013367775.1	s__Microbulbifer sp013367775	76.8772	86	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931115.1	s__Microbulbifer hydrolyticus	76.8003	85	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423345.1	s__Marinimicrobium agarilyticum	76.7999	87	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762925.1	s__Marinimicrobium koreense	76.7724	94	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	76.5052	81	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	76.2878	98	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	76.1209	87	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019225.1	s__Cellvibrio japonicus	76.0566	73	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	100.00	100.00	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,394] [INFO] GTDB search result was written to GCF_018863235.1_ASM1886323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:43,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:43,399] [INFO] DFAST_QC result json was written to GCF_018863235.1_ASM1886323v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:43,400] [INFO] DFAST_QC completed!
[2024-01-24 13:33:43,400] [INFO] Total running time: 0h1m25s