[2023-06-29 20:34:12,680] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:34:12,683] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:34:12,683] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference
[2023-06-29 20:34:14,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:34:14,390] [INFO] Task started: Prodigal
[2023-06-29 20:34:14,391] [INFO] Running command: gunzip -c /var/lib/cwl/stgeac15378-2c64-47ed-b154-be95ba0e0c57/GCA_023418355.1_ASM2341835v1_genomic.fna.gz | prodigal -d GCA_023418355.1_ASM2341835v1_genomic.fna/cds.fna -a GCA_023418355.1_ASM2341835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:34:23,309] [INFO] Task succeeded: Prodigal
[2023-06-29 20:34:23,310] [INFO] Task started: HMMsearch
[2023-06-29 20:34:23,310] [INFO] Running command: hmmsearch --tblout GCA_023418355.1_ASM2341835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference/reference_markers.hmm GCA_023418355.1_ASM2341835v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:34:23,584] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:34:23,585] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgeac15378-2c64-47ed-b154-be95ba0e0c57/GCA_023418355.1_ASM2341835v1_genomic.fna.gz]
[2023-06-29 20:34:23,615] [INFO] Query marker FASTA was written to GCA_023418355.1_ASM2341835v1_genomic.fna/markers.fasta
[2023-06-29 20:34:23,615] [INFO] Task started: Blastn
[2023-06-29 20:34:23,616] [INFO] Running command: blastn -query GCA_023418355.1_ASM2341835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference/reference_markers.fasta -out GCA_023418355.1_ASM2341835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:34:24,535] [INFO] Task succeeded: Blastn
[2023-06-29 20:34:24,539] [INFO] Selected 13 target genomes.
[2023-06-29 20:34:24,539] [INFO] Target genome list was writen to GCA_023418355.1_ASM2341835v1_genomic.fna/target_genomes.txt
[2023-06-29 20:34:24,540] [INFO] Task started: fastANI
[2023-06-29 20:34:24,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac15378-2c64-47ed-b154-be95ba0e0c57/GCA_023418355.1_ASM2341835v1_genomic.fna.gz --refList GCA_023418355.1_ASM2341835v1_genomic.fna/target_genomes.txt --output GCA_023418355.1_ASM2341835v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:34:35,968] [INFO] Task succeeded: fastANI
[2023-06-29 20:34:35,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:34:35,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:34:35,983] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:34:35,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:34:35,983] [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
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	90.4649	627	785	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	82.4764	508	785	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	81.0697	468	785	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	80.6963	469	785	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	80.2407	391	785	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	80.1499	408	785	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	80.0169	406	785	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	80.0032	397	785	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	79.9699	411	785	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.9805	336	785	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.8648	331	785	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	78.71	276	785	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.6082	193	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:34:35,985] [INFO] DFAST Taxonomy check result was written to GCA_023418355.1_ASM2341835v1_genomic.fna/tc_result.tsv
[2023-06-29 20:34:35,986] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:34:35,986] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:34:35,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference/checkm_data
[2023-06-29 20:34:35,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:34:36,030] [INFO] Task started: CheckM
[2023-06-29 20:34:36,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023418355.1_ASM2341835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023418355.1_ASM2341835v1_genomic.fna/checkm_input GCA_023418355.1_ASM2341835v1_genomic.fna/checkm_result
[2023-06-29 20:35:07,323] [INFO] Task succeeded: CheckM
[2023-06-29 20:35:07,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.12%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 20:35:07,346] [INFO] ===== Completeness check finished =====
[2023-06-29 20:35:07,346] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:35:07,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023418355.1_ASM2341835v1_genomic.fna/markers.fasta)
[2023-06-29 20:35:07,347] [INFO] Task started: Blastn
[2023-06-29 20:35:07,347] [INFO] Running command: blastn -query GCA_023418355.1_ASM2341835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa83c3f0-cb55-4935-aa47-f8df7f2c4d44/dqc_reference/reference_markers_gtdb.fasta -out GCA_023418355.1_ASM2341835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:35:09,082] [INFO] Task succeeded: Blastn
[2023-06-29 20:35:09,087] [INFO] Selected 11 target genomes.
[2023-06-29 20:35:09,088] [INFO] Target genome list was writen to GCA_023418355.1_ASM2341835v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:35:09,090] [INFO] Task started: fastANI
[2023-06-29 20:35:09,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac15378-2c64-47ed-b154-be95ba0e0c57/GCA_023418355.1_ASM2341835v1_genomic.fna.gz --refList GCA_023418355.1_ASM2341835v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023418355.1_ASM2341835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:35:17,677] [INFO] Task succeeded: fastANI
[2023-06-29 20:35:17,687] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:35:17,687] [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_008801935.1	s__Comamonas kerstersii	90.4649	627	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_000739875.1	s__Comamonas aquatica	82.4654	509	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_902829245.1	s__Comamonas jiangduensis	81.4367	357	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	95.84	95.73	0.85	0.79	3	-
GCF_900461435.1	s__Comamonas terrigena	81.0969	466	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCA_015478895.1	s__Comamonas sp015478895	80.8094	425	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836675.1	s__Comamonas sp014836675	80.6832	470	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.72	98.72	0.93	0.93	2	-
GCF_003569915.1	s__Comamonas testosteroni_D	80.2182	410	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727115.1	s__Comamonas testosteroni_E	80.0544	379	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739375.1	s__Comamonas testosteroni_B	80.0154	411	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCF_001544075.1	s__Comamonas terrae	79.9762	411	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900564145.1	s__Comamonas sp900564145	79.8176	396	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:35:17,690] [INFO] GTDB search result was written to GCA_023418355.1_ASM2341835v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:35:17,690] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:35:17,695] [INFO] DFAST_QC result json was written to GCA_023418355.1_ASM2341835v1_genomic.fna/dqc_result.json
[2023-06-29 20:35:17,696] [INFO] DFAST_QC completed!
[2023-06-29 20:35:17,696] [INFO] Total running time: 0h1m5s