[2024-01-24 14:46:57,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference
[2024-01-24 14:46:58,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,857] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg71a7fce4-8b9d-4e08-bdd5-abec7a55a230/GCF_014640395.1_ASM1464039v1_genomic.fna.gz | prodigal -d GCF_014640395.1_ASM1464039v1_genomic.fna/cds.fna -a GCF_014640395.1_ASM1464039v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:12,472] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:12,472] [INFO] Task started: HMMsearch
[2024-01-24 14:47:12,472] [INFO] Running command: hmmsearch --tblout GCF_014640395.1_ASM1464039v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference/reference_markers.hmm GCF_014640395.1_ASM1464039v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:12,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:12,842] [INFO] Found 6/6 markers.
[2024-01-24 14:47:12,898] [INFO] Query marker FASTA was written to GCF_014640395.1_ASM1464039v1_genomic.fna/markers.fasta
[2024-01-24 14:47:12,899] [INFO] Task started: Blastn
[2024-01-24 14:47:12,899] [INFO] Running command: blastn -query GCF_014640395.1_ASM1464039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference/reference_markers.fasta -out GCF_014640395.1_ASM1464039v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:13,986] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:13,990] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:13,990] [INFO] Target genome list was writen to GCF_014640395.1_ASM1464039v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:14,007] [INFO] Task started: fastANI
[2024-01-24 14:47:14,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a7fce4-8b9d-4e08-bdd5-abec7a55a230/GCF_014640395.1_ASM1464039v1_genomic.fna.gz --refList GCF_014640395.1_ASM1464039v1_genomic.fna/target_genomes.txt --output GCF_014640395.1_ASM1464039v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:25,912] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:25,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:25,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:25,923] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:47:25,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:25,923] [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
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	100.0	1379	1380	95	conclusive
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	99.9988	1373	1380	95	conclusive
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	99.9983	1378	1380	95	conclusive
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	99.9952	1375	1380	95	conclusive
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	89.9533	1094	1380	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.5442	565	1380	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.3057	563	1380	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.097	550	1380	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.0716	553	1380	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.0528	475	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:25,926] [INFO] DFAST Taxonomy check result was written to GCF_014640395.1_ASM1464039v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:25,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:25,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:25,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference/checkm_data
[2024-01-24 14:47:25,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:25,971] [INFO] Task started: CheckM
[2024-01-24 14:47:25,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640395.1_ASM1464039v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640395.1_ASM1464039v1_genomic.fna/checkm_input GCF_014640395.1_ASM1464039v1_genomic.fna/checkm_result
[2024-01-24 14:48:10,962] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:10,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:11,005] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:11,006] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:11,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640395.1_ASM1464039v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:11,006] [INFO] Task started: Blastn
[2024-01-24 14:48:11,007] [INFO] Running command: blastn -query GCF_014640395.1_ASM1464039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b4f867d-b697-4cf4-aee6-8059d72ec152/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640395.1_ASM1464039v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:12,812] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:12,816] [INFO] Selected 13 target genomes.
[2024-01-24 14:48:12,816] [INFO] Target genome list was writen to GCF_014640395.1_ASM1464039v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:12,826] [INFO] Task started: fastANI
[2024-01-24 14:48:12,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a7fce4-8b9d-4e08-bdd5-abec7a55a230/GCF_014640395.1_ASM1464039v1_genomic.fna.gz --refList GCF_014640395.1_ASM1464039v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640395.1_ASM1464039v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:24,801] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:24,812] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:24,813] [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_009908165.1	s__Frigidibacter albus	99.9988	1373	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	conclusive
GCF_001620265.1	s__Frigidibacter mobilis	89.9602	1093	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	86.8637	720	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCF_003993775.1	s__Frigidibacter sp003993775	82.2285	806	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	79.5536	563	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	79.4316	606	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_003034995.1	s__Phaeovulum veldkampii	79.3408	522	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_900005615.1	s__Paracoccus aminovorans	79.2751	548	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002356635.1	s__QY30 sp002356635	79.2705	534	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QY30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	78.9797	522	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCA_018058035.1	s__JAAKGP01 sp018058035	78.9741	512	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	78.9219	542	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787695.1	s__Paracoccus sp000787695	78.5346	473	1380	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:24,815] [INFO] GTDB search result was written to GCF_014640395.1_ASM1464039v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:24,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:24,819] [INFO] DFAST_QC result json was written to GCF_014640395.1_ASM1464039v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:24,819] [INFO] DFAST_QC completed!
[2024-01-24 14:48:24,819] [INFO] Total running time: 0h1m27s