[2023-06-29 22:35:13,015] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:35:13,017] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:35:13,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference
[2023-06-29 22:35:14,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:35:14,253] [INFO] Task started: Prodigal
[2023-06-29 22:35:14,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f1e9351-4823-4237-b744-3180beec1327/GCA_016842985.1_ASM1684298v1_genomic.fna.gz | prodigal -d GCA_016842985.1_ASM1684298v1_genomic.fna/cds.fna -a GCA_016842985.1_ASM1684298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:35:25,204] [INFO] Task succeeded: Prodigal
[2023-06-29 22:35:25,204] [INFO] Task started: HMMsearch
[2023-06-29 22:35:25,204] [INFO] Running command: hmmsearch --tblout GCA_016842985.1_ASM1684298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference/reference_markers.hmm GCA_016842985.1_ASM1684298v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:35:25,650] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:35:25,651] [INFO] Found 6/6 markers.
[2023-06-29 22:35:25,693] [INFO] Query marker FASTA was written to GCA_016842985.1_ASM1684298v1_genomic.fna/markers.fasta
[2023-06-29 22:35:25,693] [INFO] Task started: Blastn
[2023-06-29 22:35:25,693] [INFO] Running command: blastn -query GCA_016842985.1_ASM1684298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference/reference_markers.fasta -out GCA_016842985.1_ASM1684298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:35:26,432] [INFO] Task succeeded: Blastn
[2023-06-29 22:35:26,436] [INFO] Selected 32 target genomes.
[2023-06-29 22:35:26,437] [INFO] Target genome list was writen to GCA_016842985.1_ASM1684298v1_genomic.fna/target_genomes.txt
[2023-06-29 22:35:26,438] [INFO] Task started: fastANI
[2023-06-29 22:35:26,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1e9351-4823-4237-b744-3180beec1327/GCA_016842985.1_ASM1684298v1_genomic.fna.gz --refList GCA_016842985.1_ASM1684298v1_genomic.fna/target_genomes.txt --output GCA_016842985.1_ASM1684298v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:35:45,414] [INFO] Task succeeded: fastANI
[2023-06-29 22:35:45,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:35:45,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:35:45,425] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:35:45,425] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:35:45,425] [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
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	76.4136	130	1146	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.3148	71	1146	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.2951	68	1146	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.168	56	1146	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.0719	66	1146	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	75.9622	71	1146	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	75.7637	55	1146	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.652	58	1146	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.6246	68	1146	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.6142	50	1146	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:35:45,431] [INFO] DFAST Taxonomy check result was written to GCA_016842985.1_ASM1684298v1_genomic.fna/tc_result.tsv
[2023-06-29 22:35:45,432] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:35:45,432] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:35:45,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference/checkm_data
[2023-06-29 22:35:45,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:35:45,481] [INFO] Task started: CheckM
[2023-06-29 22:35:45,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016842985.1_ASM1684298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016842985.1_ASM1684298v1_genomic.fna/checkm_input GCA_016842985.1_ASM1684298v1_genomic.fna/checkm_result
[2023-06-29 22:36:23,029] [INFO] Task succeeded: CheckM
[2023-06-29 22:36:23,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 22:36:23,054] [INFO] ===== Completeness check finished =====
[2023-06-29 22:36:23,055] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:36:23,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016842985.1_ASM1684298v1_genomic.fna/markers.fasta)
[2023-06-29 22:36:23,055] [INFO] Task started: Blastn
[2023-06-29 22:36:23,056] [INFO] Running command: blastn -query GCA_016842985.1_ASM1684298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b49a07b-01f4-47d3-a3d0-5d6463bd6223/dqc_reference/reference_markers_gtdb.fasta -out GCA_016842985.1_ASM1684298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:36:24,268] [INFO] Task succeeded: Blastn
[2023-06-29 22:36:24,272] [INFO] Selected 6 target genomes.
[2023-06-29 22:36:24,273] [INFO] Target genome list was writen to GCA_016842985.1_ASM1684298v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:36:24,274] [INFO] Task started: fastANI
[2023-06-29 22:36:24,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1e9351-4823-4237-b744-3180beec1327/GCA_016842985.1_ASM1684298v1_genomic.fna.gz --refList GCA_016842985.1_ASM1684298v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016842985.1_ASM1684298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:36:30,383] [INFO] Task succeeded: fastANI
[2023-06-29 22:36:30,395] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:36:30,396] [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_003676145.1	s__Thiodiazotropha endolucinida	98.14	1021	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	conclusive
GCA_016842065.1	s__Thiodiazotropha sp016842065	94.6338	1008	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019100305.1	s__Thiodiazotropha sp019100305	93.0222	796	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001709035.1	s__Thiodiazotropha endoloripes_B	89.4996	977	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	-
GCF_001708965.1	s__Thiodiazotropha endoloripes	89.3355	980	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.62	99.43	0.97	0.94	9	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	77.8508	344	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
--------------------------------------------------------------------------------
[2023-06-29 22:36:30,398] [INFO] GTDB search result was written to GCA_016842985.1_ASM1684298v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:36:30,399] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:36:30,402] [INFO] DFAST_QC result json was written to GCA_016842985.1_ASM1684298v1_genomic.fna/dqc_result.json
[2023-06-29 22:36:30,403] [INFO] DFAST_QC completed!
[2023-06-29 22:36:30,403] [INFO] Total running time: 0h1m17s