[2024-01-24 13:32:17,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:17,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:17,638] [INFO] DQC Reference Directory: /var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference
[2024-01-24 13:32:19,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,117] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg71999a45-f214-41ff-b3b5-5cc70f764505/GCF_003933735.1_ASM393373v1_genomic.fna.gz | prodigal -d GCF_003933735.1_ASM393373v1_genomic.fna/cds.fna -a GCF_003933735.1_ASM393373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:41,225] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:41,225] [INFO] Task started: HMMsearch
[2024-01-24 13:32:41,225] [INFO] Running command: hmmsearch --tblout GCF_003933735.1_ASM393373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference/reference_markers.hmm GCF_003933735.1_ASM393373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:41,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:41,609] [INFO] Found 6/6 markers.
[2024-01-24 13:32:41,674] [INFO] Query marker FASTA was written to GCF_003933735.1_ASM393373v1_genomic.fna/markers.fasta
[2024-01-24 13:32:41,674] [INFO] Task started: Blastn
[2024-01-24 13:32:41,674] [INFO] Running command: blastn -query GCF_003933735.1_ASM393373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference/reference_markers.fasta -out GCF_003933735.1_ASM393373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:42,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:42,791] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:42,791] [INFO] Target genome list was writen to GCF_003933735.1_ASM393373v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:42,800] [INFO] Task started: fastANI
[2024-01-24 13:32:42,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg71999a45-f214-41ff-b3b5-5cc70f764505/GCF_003933735.1_ASM393373v1_genomic.fna.gz --refList GCF_003933735.1_ASM393373v1_genomic.fna/target_genomes.txt --output GCF_003933735.1_ASM393373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,226] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:55,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,226] [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	100.0	1763	1766	95	conclusive
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	82.9061	761	1766	95	below_threshold
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	82.4714	752	1766	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	82.4012	721	1766	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	82.0494	743	1766	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	81.5597	655	1766	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.1371	570	1766	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	80.0642	547	1766	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.5389	522	1766	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.4483	567	1766	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.3665	553	1766	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.184	517	1766	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,229] [INFO] DFAST Taxonomy check result was written to GCF_003933735.1_ASM393373v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference/checkm_data
[2024-01-24 13:32:55,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,296] [INFO] Task started: CheckM
[2024-01-24 13:32:55,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003933735.1_ASM393373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003933735.1_ASM393373v1_genomic.fna/checkm_input GCF_003933735.1_ASM393373v1_genomic.fna/checkm_result
[2024-01-24 13:35:02,399] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:02,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:02,423] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:02,423] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:02,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003933735.1_ASM393373v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:02,424] [INFO] Task started: Blastn
[2024-01-24 13:35:02,424] [INFO] Running command: blastn -query GCF_003933735.1_ASM393373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga73d036e-d204-4a0b-b487-9bf5cbeb1bd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003933735.1_ASM393373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:04,561] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:04,565] [INFO] Selected 12 target genomes.
[2024-01-24 13:35:04,565] [INFO] Target genome list was writen to GCF_003933735.1_ASM393373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:04,622] [INFO] Task started: fastANI
[2024-01-24 13:35:04,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg71999a45-f214-41ff-b3b5-5cc70f764505/GCF_003933735.1_ASM393373v1_genomic.fna.gz --refList GCF_003933735.1_ASM393373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003933735.1_ASM393373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:18,412] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:18,429] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:18,429] [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_003933735.1	s__Aquabacterium sp003933735	100.0	1763	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019112875.1	s__Aquabacterium excrementipullorum	88.0163	1219	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339015.1	s__Aquabacterium sp002339015	87.071	1151	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.88	99.88	0.91	0.91	2	-
GCA_001770725.1	s__Aquabacterium sp001770725	82.9352	800	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502875.1	s__Aquabacterium sp005502875	82.8379	733	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310865.1	s__Aquabacterium lacunae	82.3945	721	1766	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	82.1583	793	1766	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	82.0494	743	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963115.1	s__Aquabacterium sp003963115	81.5999	765	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909205.1	s__Aquabacterium fontiphilum	81.5949	652	1766	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	81.231	529	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	79.2761	596	1766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:18,431] [INFO] GTDB search result was written to GCF_003933735.1_ASM393373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:18,431] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:18,435] [INFO] DFAST_QC result json was written to GCF_003933735.1_ASM393373v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:18,435] [INFO] DFAST_QC completed!
[2024-01-24 13:35:18,435] [INFO] Total running time: 0h3m1s