[2024-01-24 12:45:10,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,084] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e9f7911-0478-4138-9b92-fb61b325c1fe/GCF_000520135.2_ASM52013v2_genomic.fna.gz | prodigal -d GCF_000520135.2_ASM52013v2_genomic.fna/cds.fna -a GCF_000520135.2_ASM52013v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:25,517] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:25,517] [INFO] Task started: HMMsearch
[2024-01-24 12:45:25,517] [INFO] Running command: hmmsearch --tblout GCF_000520135.2_ASM52013v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference/reference_markers.hmm GCF_000520135.2_ASM52013v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:25,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:25,791] [INFO] Found 6/6 markers.
[2024-01-24 12:45:25,833] [INFO] Query marker FASTA was written to GCF_000520135.2_ASM52013v2_genomic.fna/markers.fasta
[2024-01-24 12:45:25,833] [INFO] Task started: Blastn
[2024-01-24 12:45:25,833] [INFO] Running command: blastn -query GCF_000520135.2_ASM52013v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference/reference_markers.fasta -out GCF_000520135.2_ASM52013v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:26,889] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:26,893] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:26,893] [INFO] Target genome list was writen to GCF_000520135.2_ASM52013v2_genomic.fna/target_genomes.txt
[2024-01-24 12:45:26,900] [INFO] Task started: fastANI
[2024-01-24 12:45:26,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e9f7911-0478-4138-9b92-fb61b325c1fe/GCF_000520135.2_ASM52013v2_genomic.fna.gz --refList GCF_000520135.2_ASM52013v2_genomic.fna/target_genomes.txt --output GCF_000520135.2_ASM52013v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:40,254] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:40,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:40,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:40,266] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:40,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:40,267] [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
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	99.9988	1440	1447	95	conclusive
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	99.9768	1435	1447	95	conclusive
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	88.7511	1030	1447	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	82.0509	705	1447	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	81.961	711	1447	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	81.8793	737	1447	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	81.5792	739	1447	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	80.4015	622	1447	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	79.1643	577	1447	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	79.1074	560	1447	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6237	578	1447	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.4614	460	1447	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.4058	458	1447	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.725	380	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:40,270] [INFO] DFAST Taxonomy check result was written to GCF_000520135.2_ASM52013v2_genomic.fna/tc_result.tsv
[2024-01-24 12:45:40,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:40,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:40,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference/checkm_data
[2024-01-24 12:45:40,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:40,320] [INFO] Task started: CheckM
[2024-01-24 12:45:40,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000520135.2_ASM52013v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000520135.2_ASM52013v2_genomic.fna/checkm_input GCF_000520135.2_ASM52013v2_genomic.fna/checkm_result
[2024-01-24 12:46:24,364] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:24,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:24,392] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:24,392] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:24,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000520135.2_ASM52013v2_genomic.fna/markers.fasta)
[2024-01-24 12:46:24,393] [INFO] Task started: Blastn
[2024-01-24 12:46:24,393] [INFO] Running command: blastn -query GCF_000520135.2_ASM52013v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg126ddfd2-95c6-49d9-bccc-c7c810a56141/dqc_reference/reference_markers_gtdb.fasta -out GCF_000520135.2_ASM52013v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:26,408] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:26,412] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:26,412] [INFO] Target genome list was writen to GCF_000520135.2_ASM52013v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:26,431] [INFO] Task started: fastANI
[2024-01-24 12:46:26,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e9f7911-0478-4138-9b92-fb61b325c1fe/GCF_000520135.2_ASM52013v2_genomic.fna.gz --refList GCF_000520135.2_ASM52013v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000520135.2_ASM52013v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:34,885] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:34,893] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:34,894] [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_001633165.1	s__Rhodovulum sulfidophilum	99.9768	1436	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	conclusive
GCF_002073975.1	s__Rhodovulum sp002073975	92.1304	1213	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	88.7746	1028	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_003053725.1	s__Rhodovulum kholense	88.5712	1083	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_009649175.1	s__Rhodovulum strictum	81.9802	708	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	81.8623	738	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	81.5667	740	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	79.1273	576	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:34,896] [INFO] GTDB search result was written to GCF_000520135.2_ASM52013v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:34,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:34,900] [INFO] DFAST_QC result json was written to GCF_000520135.2_ASM52013v2_genomic.fna/dqc_result.json
[2024-01-24 12:46:34,901] [INFO] DFAST_QC completed!
[2024-01-24 12:46:34,901] [INFO] Total running time: 0h1m24s