[2024-01-24 12:44:43,735] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,737] [INFO] DQC Reference Directory: /var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference
[2024-01-24 12:44:45,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,037] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,037] [INFO] Running command: gunzip -c /var/lib/cwl/stgb62af9f9-8dae-420b-b172-dfbe5af232db/GCF_003574675.1_ASM357467v1_genomic.fna.gz | prodigal -d GCF_003574675.1_ASM357467v1_genomic.fna/cds.fna -a GCF_003574675.1_ASM357467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:56,197] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:56,198] [INFO] Task started: HMMsearch
[2024-01-24 12:44:56,198] [INFO] Running command: hmmsearch --tblout GCF_003574675.1_ASM357467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference/reference_markers.hmm GCF_003574675.1_ASM357467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:56,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:56,493] [INFO] Found 6/6 markers.
[2024-01-24 12:44:56,531] [INFO] Query marker FASTA was written to GCF_003574675.1_ASM357467v1_genomic.fna/markers.fasta
[2024-01-24 12:44:56,532] [INFO] Task started: Blastn
[2024-01-24 12:44:56,532] [INFO] Running command: blastn -query GCF_003574675.1_ASM357467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference/reference_markers.fasta -out GCF_003574675.1_ASM357467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:57,776] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:57,779] [INFO] Selected 18 target genomes.
[2024-01-24 12:44:57,780] [INFO] Target genome list was writen to GCF_003574675.1_ASM357467v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:57,789] [INFO] Task started: fastANI
[2024-01-24 12:44:57,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62af9f9-8dae-420b-b172-dfbe5af232db/GCF_003574675.1_ASM357467v1_genomic.fna.gz --refList GCF_003574675.1_ASM357467v1_genomic.fna/target_genomes.txt --output GCF_003574675.1_ASM357467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:18,429] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:18,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:18,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:18,448] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:18,449] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:18,449] [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	82.3434	699	1200	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	82.2566	718	1200	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	81.9758	748	1200	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	81.8818	749	1200	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	81.4494	667	1200	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	81.446	651	1200	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	81.4354	656	1200	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.6925	746	1200	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.5867	637	1200	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.4947	723	1200	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.4461	652	1200	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.4217	718	1200	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	80.0229	648	1200	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.7025	655	1200	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.6461	651	1200	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.6331	531	1200	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.4943	584	1200	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.4051	515	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,451] [INFO] DFAST Taxonomy check result was written to GCF_003574675.1_ASM357467v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:18,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:18,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:18,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference/checkm_data
[2024-01-24 12:45:18,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:18,496] [INFO] Task started: CheckM
[2024-01-24 12:45:18,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574675.1_ASM357467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574675.1_ASM357467v1_genomic.fna/checkm_input GCF_003574675.1_ASM357467v1_genomic.fna/checkm_result
[2024-01-24 12:46:17,270] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:17,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:17,292] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:17,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:17,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574675.1_ASM357467v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:17,293] [INFO] Task started: Blastn
[2024-01-24 12:46:17,293] [INFO] Running command: blastn -query GCF_003574675.1_ASM357467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf07b69a2-3e68-4410-bc75-6fd61f4ec388/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574675.1_ASM357467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:19,709] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:19,714] [INFO] Selected 23 target genomes.
[2024-01-24 12:46:19,714] [INFO] Target genome list was writen to GCF_003574675.1_ASM357467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:19,771] [INFO] Task started: fastANI
[2024-01-24 12:46:19,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62af9f9-8dae-420b-b172-dfbe5af232db/GCF_003574675.1_ASM357467v1_genomic.fna.gz --refList GCF_003574675.1_ASM357467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574675.1_ASM357467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:47,672] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:47,702] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:47,703] [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_003574675.1	s__Calidifontimicrobium sediminis	100.0	1196	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	conclusive
GCA_001725505.1	s__Rubrivivax sp001725505	82.6638	663	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	82.3866	695	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCA_017302495.1	s__Rubrivivax sp017302495	82.2204	648	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	82.0617	826	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716535.1	s__Rubrivivax sp016716535	82.013	802	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	81.9545	684	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075165.1	s__JAEUPI01 sp015075165	81.3244	742	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAEUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	81.3113	815	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	81.2891	647	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724995.1	s__Rubrivivax sp001724995	81.2646	674	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	81.2155	579	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075545.1	s__JAEUPI01 sp008933545	81.0366	627	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAEUPI01	95.0	98.97	98.97	0.77	0.77	2	-
GCF_000015725.1	s__Methylibium petroleiphilum	80.9436	643	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	96.91	96.03	0.83	0.81	5	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	80.7164	770	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	80.6931	746	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790425.1	s__Rubrivivax sp016790425	80.6572	638	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294065.1	s__Sphaerotilus sp013294065	80.5784	720	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	80.4539	714	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	80.4363	706	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.319	725	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232985.1	s__JAFAMW01 sp019232985	80.0733	505	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289985.1	s__CAIMXF01 sp013289985	79.9731	610	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIMXF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:47,704] [INFO] GTDB search result was written to GCF_003574675.1_ASM357467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:47,709] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:47,713] [INFO] DFAST_QC result json was written to GCF_003574675.1_ASM357467v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:47,713] [INFO] DFAST_QC completed!
[2024-01-24 12:46:47,713] [INFO] Total running time: 0h2m4s