[2023-06-30 18:31:30,442] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:31:30,800] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:31:30,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference
[2023-06-30 18:31:32,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:31:32,762] [INFO] Task started: Prodigal
[2023-06-30 18:31:32,763] [INFO] Running command: gunzip -c /var/lib/cwl/stge3619f9d-d4b0-42b9-9a00-55ed218be260/GCA_024708905.1_ASM2470890v1_genomic.fna.gz | prodigal -d GCA_024708905.1_ASM2470890v1_genomic.fna/cds.fna -a GCA_024708905.1_ASM2470890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:31:43,162] [INFO] Task succeeded: Prodigal
[2023-06-30 18:31:43,163] [INFO] Task started: HMMsearch
[2023-06-30 18:31:43,163] [INFO] Running command: hmmsearch --tblout GCA_024708905.1_ASM2470890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference/reference_markers.hmm GCA_024708905.1_ASM2470890v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:31:43,432] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:31:43,434] [INFO] Found 6/6 markers.
[2023-06-30 18:31:43,470] [INFO] Query marker FASTA was written to GCA_024708905.1_ASM2470890v1_genomic.fna/markers.fasta
[2023-06-30 18:31:43,471] [INFO] Task started: Blastn
[2023-06-30 18:31:43,471] [INFO] Running command: blastn -query GCA_024708905.1_ASM2470890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference/reference_markers.fasta -out GCA_024708905.1_ASM2470890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:31:44,524] [INFO] Task succeeded: Blastn
[2023-06-30 18:31:44,529] [INFO] Selected 15 target genomes.
[2023-06-30 18:31:44,530] [INFO] Target genome list was writen to GCA_024708905.1_ASM2470890v1_genomic.fna/target_genomes.txt
[2023-06-30 18:31:44,532] [INFO] Task started: fastANI
[2023-06-30 18:31:44,532] [INFO] Running command: fastANI --query /var/lib/cwl/stge3619f9d-d4b0-42b9-9a00-55ed218be260/GCA_024708905.1_ASM2470890v1_genomic.fna.gz --refList GCA_024708905.1_ASM2470890v1_genomic.fna/target_genomes.txt --output GCA_024708905.1_ASM2470890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:31:57,127] [INFO] Task succeeded: fastANI
[2023-06-30 18:31:57,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:31:57,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:31:57,145] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:31:57,145] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:31:57,145] [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 flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	84.1645	778	1260	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	84.0155	770	1260	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	83.935	767	1260	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	80.6834	612	1260	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	80.5499	653	1260	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.373	660	1260	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.3641	661	1260	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.8365	545	1260	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.7125	560	1260	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	79.5289	574	1260	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	79.5196	571	1260	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.353	573	1260	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	79.2714	539	1260	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.2412	505	1260	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.6979	477	1260	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:31:57,147] [INFO] DFAST Taxonomy check result was written to GCA_024708905.1_ASM2470890v1_genomic.fna/tc_result.tsv
[2023-06-30 18:31:57,148] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:31:57,148] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:31:57,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference/checkm_data
[2023-06-30 18:31:57,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:31:57,195] [INFO] Task started: CheckM
[2023-06-30 18:31:57,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708905.1_ASM2470890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708905.1_ASM2470890v1_genomic.fna/checkm_input GCA_024708905.1_ASM2470890v1_genomic.fna/checkm_result
[2023-06-30 18:32:33,512] [INFO] Task succeeded: CheckM
[2023-06-30 18:32:33,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:32:33,535] [INFO] ===== Completeness check finished =====
[2023-06-30 18:32:33,535] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:32:33,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708905.1_ASM2470890v1_genomic.fna/markers.fasta)
[2023-06-30 18:32:33,536] [INFO] Task started: Blastn
[2023-06-30 18:32:33,536] [INFO] Running command: blastn -query GCA_024708905.1_ASM2470890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg433b85e0-0508-4749-a462-8651c82becd0/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708905.1_ASM2470890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:35,516] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:35,521] [INFO] Selected 11 target genomes.
[2023-06-30 18:32:35,521] [INFO] Target genome list was writen to GCA_024708905.1_ASM2470890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:32:35,554] [INFO] Task started: fastANI
[2023-06-30 18:32:35,555] [INFO] Running command: fastANI --query /var/lib/cwl/stge3619f9d-d4b0-42b9-9a00-55ed218be260/GCA_024708905.1_ASM2470890v1_genomic.fna.gz --refList GCA_024708905.1_ASM2470890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708905.1_ASM2470890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:32:45,248] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:45,262] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:32:45,262] [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_015999335.1	s__Tabrizicola soli	99.0208	1231	1260	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_002900975.1	s__Tabrizicola aquatica	85.1591	892	1260	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	84.6688	827	1260	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	84.1603	778	1260	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	84.1194	588	1260	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	84.1012	780	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011174775.1	s__Tabrizicola sp011174775	83.9969	771	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574395.1	s__Tabrizicola thermarum	83.93	767	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	97.33	97.31	0.93	0.92	4	-
GCA_017303485.1	s__Tabrizicola sp017303485	83.5904	780	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762095.1	s__Tabrizicola sp004762095	82.5899	762	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	99.01	99.01	0.96	0.96	2	-
GCA_016792685.1	s__Tabrizicola sp016792685	82.129	691	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:32:45,265] [INFO] GTDB search result was written to GCA_024708905.1_ASM2470890v1_genomic.fna/result_gtdb.tsv
[2023-06-30 18:32:45,265] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:32:45,269] [INFO] DFAST_QC result json was written to GCA_024708905.1_ASM2470890v1_genomic.fna/dqc_result.json
[2023-06-30 18:32:45,269] [INFO] DFAST_QC completed!
[2023-06-30 18:32:45,269] [INFO] Total running time: 0h1m15s