[2024-01-25 20:12:35,669] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:35,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:35,670] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference
[2024-01-25 20:12:36,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:36,808] [INFO] Task started: Prodigal
[2024-01-25 20:12:36,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg3088f52a-42d0-4719-928e-51a4a8ef151f/GCF_002900975.1_ASM290097v1_genomic.fna.gz | prodigal -d GCF_002900975.1_ASM290097v1_genomic.fna/cds.fna -a GCF_002900975.1_ASM290097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:47,088] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:47,089] [INFO] Task started: HMMsearch
[2024-01-25 20:12:47,089] [INFO] Running command: hmmsearch --tblout GCF_002900975.1_ASM290097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference/reference_markers.hmm GCF_002900975.1_ASM290097v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:47,314] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:47,315] [INFO] Found 6/6 markers.
[2024-01-25 20:12:47,346] [INFO] Query marker FASTA was written to GCF_002900975.1_ASM290097v1_genomic.fna/markers.fasta
[2024-01-25 20:12:47,346] [INFO] Task started: Blastn
[2024-01-25 20:12:47,346] [INFO] Running command: blastn -query GCF_002900975.1_ASM290097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference/reference_markers.fasta -out GCF_002900975.1_ASM290097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:48,280] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:48,282] [INFO] Selected 14 target genomes.
[2024-01-25 20:12:48,283] [INFO] Target genome list was writen to GCF_002900975.1_ASM290097v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:48,289] [INFO] Task started: fastANI
[2024-01-25 20:12:48,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg3088f52a-42d0-4719-928e-51a4a8ef151f/GCF_002900975.1_ASM290097v1_genomic.fna.gz --refList GCF_002900975.1_ASM290097v1_genomic.fna/target_genomes.txt --output GCF_002900975.1_ASM290097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:00,657] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:00,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:00,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:00,667] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:00,667] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:00,667] [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 calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	83.7275	846	1283	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	83.6981	860	1283	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	83.5637	871	1283	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.7949	663	1283	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.6251	637	1283	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.5841	637	1283	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.4107	576	1283	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.2098	583	1283	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.0785	539	1283	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	79.0286	530	1283	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.0074	531	1283	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.9905	590	1283	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.9319	549	1283	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	78.867	450	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:00,669] [INFO] DFAST Taxonomy check result was written to GCF_002900975.1_ASM290097v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:00,669] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:00,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:00,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference/checkm_data
[2024-01-25 20:13:00,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:00,708] [INFO] Task started: CheckM
[2024-01-25 20:13:00,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002900975.1_ASM290097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002900975.1_ASM290097v1_genomic.fna/checkm_input GCF_002900975.1_ASM290097v1_genomic.fna/checkm_result
[2024-01-25 20:13:35,971] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:35,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:36,011] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:36,011] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:36,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002900975.1_ASM290097v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:36,012] [INFO] Task started: Blastn
[2024-01-25 20:13:36,012] [INFO] Running command: blastn -query GCF_002900975.1_ASM290097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8b948f-bce6-4d97-a491-7532dbfe3240/dqc_reference/reference_markers_gtdb.fasta -out GCF_002900975.1_ASM290097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:37,826] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:37,828] [INFO] Selected 11 target genomes.
[2024-01-25 20:13:37,829] [INFO] Target genome list was writen to GCF_002900975.1_ASM290097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:37,843] [INFO] Task started: fastANI
[2024-01-25 20:13:37,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg3088f52a-42d0-4719-928e-51a4a8ef151f/GCF_002900975.1_ASM290097v1_genomic.fna.gz --refList GCF_002900975.1_ASM290097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002900975.1_ASM290097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:47,997] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:48,004] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:48,004] [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_002900975.1	s__Tabrizicola aquatica	100.0	1282	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015999335.1	s__Tabrizicola soli	85.0903	960	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824055.1	s__Tabrizicola sp013824055	84.1286	606	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	98.98	98.98	0.93	0.93	2	-
GCF_011174775.1	s__Tabrizicola sp011174775	83.7233	845	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	83.5787	870	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222785.1	s__Tabrizicola sp005222785	83.5766	903	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793705.1	s__Tabrizicola sp016793705	83.4014	840	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057165.1	s__Tabrizicola sp018057165	83.3982	574	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303485.1	s__Tabrizicola sp017303485	83.0994	781	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	83.0757	788	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792685.1	s__Tabrizicola sp016792685	82.0053	720	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:48,006] [INFO] GTDB search result was written to GCF_002900975.1_ASM290097v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:48,007] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:48,010] [INFO] DFAST_QC result json was written to GCF_002900975.1_ASM290097v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:48,010] [INFO] DFAST_QC completed!
[2024-01-25 20:13:48,010] [INFO] Total running time: 0h1m12s