[2024-01-24 14:46:55,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,077] [INFO] DQC Reference Directory: /var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference
[2024-01-24 14:46:58,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,018] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f37c335-56a7-47f1-beef-2a47cd46ccfc/GCF_003254295.1_ASM325429v1_genomic.fna.gz | prodigal -d GCF_003254295.1_ASM325429v1_genomic.fna/cds.fna -a GCF_003254295.1_ASM325429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:09,041] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:09,042] [INFO] Task started: HMMsearch
[2024-01-24 14:47:09,042] [INFO] Running command: hmmsearch --tblout GCF_003254295.1_ASM325429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference/reference_markers.hmm GCF_003254295.1_ASM325429v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:09,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:09,335] [INFO] Found 6/6 markers.
[2024-01-24 14:47:09,380] [INFO] Query marker FASTA was written to GCF_003254295.1_ASM325429v1_genomic.fna/markers.fasta
[2024-01-24 14:47:09,381] [INFO] Task started: Blastn
[2024-01-24 14:47:09,381] [INFO] Running command: blastn -query GCF_003254295.1_ASM325429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference/reference_markers.fasta -out GCF_003254295.1_ASM325429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:10,441] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:10,445] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:10,445] [INFO] Target genome list was writen to GCF_003254295.1_ASM325429v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:10,453] [INFO] Task started: fastANI
[2024-01-24 14:47:10,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f37c335-56a7-47f1-beef-2a47cd46ccfc/GCF_003254295.1_ASM325429v1_genomic.fna.gz --refList GCF_003254295.1_ASM325429v1_genomic.fna/target_genomes.txt --output GCF_003254295.1_ASM325429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:23,874] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:23,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:23,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:23,899] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:23,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:23,900] [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
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	100.0	1212	1213	95	conclusive
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	89.3363	968	1213	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	82.0799	683	1213	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	81.8974	693	1213	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	81.7042	698	1213	95	below_threshold
Rhodobacter aestuarii	strain=DSM 19945	GCA_900156655.1	453582	453582	type	True	80.2627	683	1213	95	below_threshold
Rhodobacter aestuarii	strain=JA296	GCA_003053525.1	453582	453582	type	True	80.2598	676	1213	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	79.2496	557	1213	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.2436	559	1213	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.0583	512	1213	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.0552	507	1213	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.0385	471	1213	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.891	574	1213	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.7082	490	1213	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.6349	412	1213	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	78.0089	424	1213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:23,901] [INFO] DFAST Taxonomy check result was written to GCF_003254295.1_ASM325429v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:23,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:23,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:23,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference/checkm_data
[2024-01-24 14:47:23,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:23,943] [INFO] Task started: CheckM
[2024-01-24 14:47:23,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254295.1_ASM325429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254295.1_ASM325429v1_genomic.fna/checkm_input GCF_003254295.1_ASM325429v1_genomic.fna/checkm_result
[2024-01-24 14:48:23,790] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:23,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:23,812] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:23,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:23,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254295.1_ASM325429v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:23,813] [INFO] Task started: Blastn
[2024-01-24 14:48:23,814] [INFO] Running command: blastn -query GCF_003254295.1_ASM325429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6eab5b9-a32a-41ec-9b58-5604107a0a76/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254295.1_ASM325429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:25,752] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:25,756] [INFO] Selected 8 target genomes.
[2024-01-24 14:48:25,756] [INFO] Target genome list was writen to GCF_003254295.1_ASM325429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:25,763] [INFO] Task started: fastANI
[2024-01-24 14:48:25,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f37c335-56a7-47f1-beef-2a47cd46ccfc/GCF_003254295.1_ASM325429v1_genomic.fna.gz --refList GCF_003254295.1_ASM325429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254295.1_ASM325429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:33,018] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:33,032] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:33,032] [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_003254295.1	s__Rhodobacter capsulatus	100.0	1212	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	conclusive
GCF_005144475.1	s__Rhodobacter capsulatus_C	94.5722	1015	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021865.1	s__Rhodobacter capsulatus_B	93.8305	1085	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.13	98.02	0.96	0.92	8	-
GCF_003217355.1	s__Rhodobacter viridis	89.3656	966	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900217815.1	s__Rhodobacter maris	82.6342	821	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	82.1981	561	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249215.1	s__SZUA-611 sp003249215	81.5084	556	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	81.2572	649	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:33,033] [INFO] GTDB search result was written to GCF_003254295.1_ASM325429v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:33,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:33,038] [INFO] DFAST_QC result json was written to GCF_003254295.1_ASM325429v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:33,039] [INFO] DFAST_QC completed!
[2024-01-24 14:48:33,039] [INFO] Total running time: 0h1m38s