[2023-06-17 00:12:35,319] [INFO] DFAST_QC pipeline started.
[2023-06-17 00:12:35,321] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 00:12:35,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference
[2023-06-17 00:12:36,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 00:12:36,629] [INFO] Task started: Prodigal
[2023-06-17 00:12:36,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg536b42d9-4f85-4322-be8e-628cdfefb624/GCA_028868855.1_ASM2886885v1_genomic.fna.gz | prodigal -d GCA_028868855.1_ASM2886885v1_genomic.fna/cds.fna -a GCA_028868855.1_ASM2886885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 00:12:49,170] [INFO] Task succeeded: Prodigal
[2023-06-17 00:12:49,170] [INFO] Task started: HMMsearch
[2023-06-17 00:12:49,170] [INFO] Running command: hmmsearch --tblout GCA_028868855.1_ASM2886885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference/reference_markers.hmm GCA_028868855.1_ASM2886885v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 00:12:49,467] [INFO] Task succeeded: HMMsearch
[2023-06-17 00:12:49,468] [INFO] Found 6/6 markers.
[2023-06-17 00:12:49,501] [INFO] Query marker FASTA was written to GCA_028868855.1_ASM2886885v1_genomic.fna/markers.fasta
[2023-06-17 00:12:49,502] [INFO] Task started: Blastn
[2023-06-17 00:12:49,502] [INFO] Running command: blastn -query GCA_028868855.1_ASM2886885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference/reference_markers.fasta -out GCA_028868855.1_ASM2886885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:12:50,468] [INFO] Task succeeded: Blastn
[2023-06-17 00:12:50,472] [INFO] Selected 19 target genomes.
[2023-06-17 00:12:50,473] [INFO] Target genome list was writen to GCA_028868855.1_ASM2886885v1_genomic.fna/target_genomes.txt
[2023-06-17 00:12:50,480] [INFO] Task started: fastANI
[2023-06-17 00:12:50,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg536b42d9-4f85-4322-be8e-628cdfefb624/GCA_028868855.1_ASM2886885v1_genomic.fna.gz --refList GCA_028868855.1_ASM2886885v1_genomic.fna/target_genomes.txt --output GCA_028868855.1_ASM2886885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 00:13:05,625] [INFO] Task succeeded: fastANI
[2023-06-17 00:13:05,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 00:13:05,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 00:13:05,644] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 00:13:05,645] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 00:13:05,645] [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
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	80.9405	532	1125	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	80.812	560	1125	95	below_threshold
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	80.5334	523	1125	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	80.3551	518	1125	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	80.2747	468	1125	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	79.9741	442	1125	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.7751	343	1125	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.47	332	1125	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.427	305	1125	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	78.4092	313	1125	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	78.3824	330	1125	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.2607	297	1125	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.2385	313	1125	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	78.2253	311	1125	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.0823	275	1125	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.076	288	1125	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.0604	323	1125	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	77.4821	199	1125	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	77.3716	193	1125	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 00:13:05,648] [INFO] DFAST Taxonomy check result was written to GCA_028868855.1_ASM2886885v1_genomic.fna/tc_result.tsv
[2023-06-17 00:13:05,648] [INFO] ===== Taxonomy check completed =====
[2023-06-17 00:13:05,648] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 00:13:05,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference/checkm_data
[2023-06-17 00:13:05,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 00:13:05,685] [INFO] Task started: CheckM
[2023-06-17 00:13:05,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028868855.1_ASM2886885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028868855.1_ASM2886885v1_genomic.fna/checkm_input GCA_028868855.1_ASM2886885v1_genomic.fna/checkm_result
[2023-06-17 00:13:57,834] [INFO] Task succeeded: CheckM
[2023-06-17 00:13:57,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 00:13:57,859] [INFO] ===== Completeness check finished =====
[2023-06-17 00:13:57,859] [INFO] ===== Start GTDB Search =====
[2023-06-17 00:13:57,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028868855.1_ASM2886885v1_genomic.fna/markers.fasta)
[2023-06-17 00:13:57,860] [INFO] Task started: Blastn
[2023-06-17 00:13:57,860] [INFO] Running command: blastn -query GCA_028868855.1_ASM2886885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e25c6c4-9585-4674-909b-e9b7d5ceb6f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_028868855.1_ASM2886885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:13:59,704] [INFO] Task succeeded: Blastn
[2023-06-17 00:13:59,710] [INFO] Selected 17 target genomes.
[2023-06-17 00:13:59,710] [INFO] Target genome list was writen to GCA_028868855.1_ASM2886885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 00:13:59,728] [INFO] Task started: fastANI
[2023-06-17 00:13:59,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg536b42d9-4f85-4322-be8e-628cdfefb624/GCA_028868855.1_ASM2886885v1_genomic.fna.gz --refList GCA_028868855.1_ASM2886885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028868855.1_ASM2886885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 00:14:12,896] [INFO] Task succeeded: fastANI
[2023-06-17 00:14:12,923] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 00:14:12,924] [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_013822685.1	s__Aquabacterium sp013822685	81.7147	590	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378415.1	s__Aquabacterium sp014378415	81.6753	575	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195855.1	s__Aquabacterium sp016195855	81.0546	591	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768065.1	s__Aquabacterium sp000768065	81.0518	619	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770725.1	s__Aquabacterium sp001770725	80.9595	546	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989885.1	s__Aquabacterium sp017989885	80.8725	285	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	98.47	98.47	0.69	0.69	2	-
GCF_004362855.1	s__Aquabacterium commune	80.83	558	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	95.44	95.44	0.90	0.90	2	-
GCA_001770775.1	s__Aquabacterium sp001770775	80.702	511	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003963115.1	s__Aquabacterium sp003963115	80.6782	572	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447195.1	s__Aquabacterium parvum	80.5338	523	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
GCA_019112875.1	s__Aquabacterium excrementipullorum	80.4126	515	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003100395.1	s__Aquabacterium olei	80.3623	517	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000265.1	s__Aquabacterium sp016000265	80.3469	516	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_017994835.1	s__Aquabacterium sp017994835	80.2919	399	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.70	99.70	0.89	0.89	2	-
GCF_004310865.1	s__Aquabacterium lacunae	80.2802	467	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185075.1	s__Aquabacterium sp016185075	80.2156	402	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234775.1	s__Aquabacterium sp016234775	80.0595	511	1125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 00:14:12,927] [INFO] GTDB search result was written to GCA_028868855.1_ASM2886885v1_genomic.fna/result_gtdb.tsv
[2023-06-17 00:14:12,927] [INFO] ===== GTDB Search completed =====
[2023-06-17 00:14:12,931] [INFO] DFAST_QC result json was written to GCA_028868855.1_ASM2886885v1_genomic.fna/dqc_result.json
[2023-06-17 00:14:12,931] [INFO] DFAST_QC completed!
[2023-06-17 00:14:12,932] [INFO] Total running time: 0h1m38s