[2024-01-24 14:07:30,860] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:30,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:30,862] [INFO] DQC Reference Directory: /var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference
[2024-01-24 14:07:32,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,133] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg307baa53-7247-4df7-98c0-31a8deec78b1/GCF_004016505.1_ASM401650v1_genomic.fna.gz | prodigal -d GCF_004016505.1_ASM401650v1_genomic.fna/cds.fna -a GCF_004016505.1_ASM401650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:48,825] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:48,826] [INFO] Task started: HMMsearch
[2024-01-24 14:07:48,826] [INFO] Running command: hmmsearch --tblout GCF_004016505.1_ASM401650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference/reference_markers.hmm GCF_004016505.1_ASM401650v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:49,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:49,141] [INFO] Found 6/6 markers.
[2024-01-24 14:07:49,193] [INFO] Query marker FASTA was written to GCF_004016505.1_ASM401650v1_genomic.fna/markers.fasta
[2024-01-24 14:07:49,194] [INFO] Task started: Blastn
[2024-01-24 14:07:49,194] [INFO] Running command: blastn -query GCF_004016505.1_ASM401650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference/reference_markers.fasta -out GCF_004016505.1_ASM401650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:50,300] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:50,305] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:50,305] [INFO] Target genome list was writen to GCF_004016505.1_ASM401650v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:50,320] [INFO] Task started: fastANI
[2024-01-24 14:07:50,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg307baa53-7247-4df7-98c0-31a8deec78b1/GCF_004016505.1_ASM401650v1_genomic.fna.gz --refList GCF_004016505.1_ASM401650v1_genomic.fna/target_genomes.txt --output GCF_004016505.1_ASM401650v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:11,584] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:11,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:11,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:11,600] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:08:11,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:08:11,600] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.4648	736	1635	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	81.445	766	1635	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	81.1481	799	1635	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	81.1183	816	1635	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.1958	632	1635	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.165	660	1635	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.0288	652	1635	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.0207	647	1635	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.0043	806	1635	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.9636	738	1635	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.8287	649	1635	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.8009	728	1635	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.7306	742	1635	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.7259	652	1635	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.7198	620	1635	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.5886	618	1635	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.5428	619	1635	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.1802	559	1635	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.1098	618	1635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:11,602] [INFO] DFAST Taxonomy check result was written to GCF_004016505.1_ASM401650v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:11,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:11,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:11,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference/checkm_data
[2024-01-24 14:08:11,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:11,656] [INFO] Task started: CheckM
[2024-01-24 14:08:11,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004016505.1_ASM401650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004016505.1_ASM401650v1_genomic.fna/checkm_input GCF_004016505.1_ASM401650v1_genomic.fna/checkm_result
[2024-01-24 14:10:06,548] [INFO] Task succeeded: CheckM
[2024-01-24 14:10:06,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:10:06,571] [INFO] ===== Completeness check finished =====
[2024-01-24 14:10:06,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:10:06,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004016505.1_ASM401650v1_genomic.fna/markers.fasta)
[2024-01-24 14:10:06,572] [INFO] Task started: Blastn
[2024-01-24 14:10:06,572] [INFO] Running command: blastn -query GCF_004016505.1_ASM401650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg109b3761-cc04-4108-b3c0-7867255c88e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004016505.1_ASM401650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:08,758] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:08,762] [INFO] Selected 10 target genomes.
[2024-01-24 14:10:08,762] [INFO] Target genome list was writen to GCF_004016505.1_ASM401650v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:10:08,792] [INFO] Task started: fastANI
[2024-01-24 14:10:08,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg307baa53-7247-4df7-98c0-31a8deec78b1/GCF_004016505.1_ASM401650v1_genomic.fna.gz --refList GCF_004016505.1_ASM401650v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004016505.1_ASM401650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:21,645] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:21,659] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:21,660] [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_004016505.1	s__Rubrivivax rivuli	100.0	1635	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001295865.1	s__Rubrivivax sp001295865	91.1188	1301	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001295905.1	s__Rubrivivax sp001295905	87.7358	1181	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822265.1	s__Rubrivivax sp013822265	84.397	871	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704535.1	s__Rubrivivax sp016704535	84.241	865	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828235.1	s__Rubrivivax sp903828235	83.4452	864	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.94	99.91	0.96	0.96	5	-
GCA_903914615.1	s__Rubrivivax sp903914615	83.0344	795	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904426505.1	s__Rubrivivax sp904426505	82.4164	917	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464055.1	s__Rubrivivax sp001464055	81.6008	888	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790225.1	s__Rubrivivax sp016790225	80.4322	704	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:10:21,661] [INFO] GTDB search result was written to GCF_004016505.1_ASM401650v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:21,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:21,665] [INFO] DFAST_QC result json was written to GCF_004016505.1_ASM401650v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:21,665] [INFO] DFAST_QC completed!
[2024-01-24 14:10:21,665] [INFO] Total running time: 0h2m51s