[2024-01-25 18:04:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:35,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:35,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference
[2024-01-25 18:04:36,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:36,680] [INFO] Task started: Prodigal
[2024-01-25 18:04:36,680] [INFO] Running command: gunzip -c /var/lib/cwl/stgef2f29c0-950d-4bed-99b8-2ca0daf74f88/GCF_009908165.1_ASM990816v1_genomic.fna.gz | prodigal -d GCF_009908165.1_ASM990816v1_genomic.fna/cds.fna -a GCF_009908165.1_ASM990816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:47,837] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:47,837] [INFO] Task started: HMMsearch
[2024-01-25 18:04:47,837] [INFO] Running command: hmmsearch --tblout GCF_009908165.1_ASM990816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference/reference_markers.hmm GCF_009908165.1_ASM990816v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:48,126] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:48,127] [INFO] Found 6/6 markers.
[2024-01-25 18:04:48,168] [INFO] Query marker FASTA was written to GCF_009908165.1_ASM990816v1_genomic.fna/markers.fasta
[2024-01-25 18:04:48,168] [INFO] Task started: Blastn
[2024-01-25 18:04:48,168] [INFO] Running command: blastn -query GCF_009908165.1_ASM990816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference/reference_markers.fasta -out GCF_009908165.1_ASM990816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:49,112] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:49,114] [INFO] Selected 10 target genomes.
[2024-01-25 18:04:49,115] [INFO] Target genome list was writen to GCF_009908165.1_ASM990816v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:49,120] [INFO] Task started: fastANI
[2024-01-25 18:04:49,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgef2f29c0-950d-4bed-99b8-2ca0daf74f88/GCF_009908165.1_ASM990816v1_genomic.fna.gz --refList GCF_009908165.1_ASM990816v1_genomic.fna/target_genomes.txt --output GCF_009908165.1_ASM990816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:59,456] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:59,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:59,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:59,463] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:04:59,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:59,464] [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=SP32	GCA_009908165.1	1465486	1465486	type	True	100.0	1373	1376	95	conclusive
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	99.9969	1364	1376	95	conclusive
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	99.9963	1373	1376	95	conclusive
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	99.9958	1366	1376	95	conclusive
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	89.9965	1077	1376	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.5347	569	1376	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.3286	560	1376	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.1081	472	1376	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.0332	557	1376	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.0246	558	1376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:59,465] [INFO] DFAST Taxonomy check result was written to GCF_009908165.1_ASM990816v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:59,466] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:59,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:59,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference/checkm_data
[2024-01-25 18:04:59,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:59,507] [INFO] Task started: CheckM
[2024-01-25 18:04:59,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009908165.1_ASM990816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009908165.1_ASM990816v1_genomic.fna/checkm_input GCF_009908165.1_ASM990816v1_genomic.fna/checkm_result
[2024-01-25 18:05:42,859] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:42,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:42,876] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:42,876] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:42,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009908165.1_ASM990816v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:42,877] [INFO] Task started: Blastn
[2024-01-25 18:05:42,877] [INFO] Running command: blastn -query GCF_009908165.1_ASM990816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc611a1-9d99-41d1-acd5-2f110d288607/dqc_reference/reference_markers_gtdb.fasta -out GCF_009908165.1_ASM990816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:44,589] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:44,592] [INFO] Selected 13 target genomes.
[2024-01-25 18:05:44,592] [INFO] Target genome list was writen to GCF_009908165.1_ASM990816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:44,606] [INFO] Task started: fastANI
[2024-01-25 18:05:44,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgef2f29c0-950d-4bed-99b8-2ca0daf74f88/GCF_009908165.1_ASM990816v1_genomic.fna.gz --refList GCF_009908165.1_ASM990816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009908165.1_ASM990816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:56,761] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:56,769] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:56,769] [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	100.0	1373	1376	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	89.9882	1077	1376	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	86.8036	709	1376	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	82.2299	803	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	79.5023	522	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	79.4858	567	1376	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	79.4561	605	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_900005615.1	s__Paracoccus aminovorans	79.2817	542	1376	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	79.2552	531	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QY30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	79.0549	508	1376	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	78.9915	536	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	78.7022	541	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_000787695.1	s__Paracoccus sp000787695	78.5962	462	1376	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:56,771] [INFO] GTDB search result was written to GCF_009908165.1_ASM990816v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:56,771] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:56,774] [INFO] DFAST_QC result json was written to GCF_009908165.1_ASM990816v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:56,774] [INFO] DFAST_QC completed!
[2024-01-25 18:05:56,774] [INFO] Total running time: 0h1m21s