[2024-01-24 14:28:08,476] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference
[2024-01-24 14:28:10,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,421] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg170a4326-fbd2-4a26-81c2-5b3e99188a23/GCF_900637555.1_51726_E01_genomic.fna.gz | prodigal -d GCF_900637555.1_51726_E01_genomic.fna/cds.fna -a GCF_900637555.1_51726_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:21,598] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:21,598] [INFO] Task started: HMMsearch
[2024-01-24 14:28:21,598] [INFO] Running command: hmmsearch --tblout GCF_900637555.1_51726_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference/reference_markers.hmm GCF_900637555.1_51726_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:21,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:21,971] [INFO] Found 6/6 markers.
[2024-01-24 14:28:22,003] [INFO] Query marker FASTA was written to GCF_900637555.1_51726_E01_genomic.fna/markers.fasta
[2024-01-24 14:28:22,004] [INFO] Task started: Blastn
[2024-01-24 14:28:22,004] [INFO] Running command: blastn -query GCF_900637555.1_51726_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference/reference_markers.fasta -out GCF_900637555.1_51726_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:23,082] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:23,085] [INFO] Selected 20 target genomes.
[2024-01-24 14:28:23,085] [INFO] Target genome list was writen to GCF_900637555.1_51726_E01_genomic.fna/target_genomes.txt
[2024-01-24 14:28:23,107] [INFO] Task started: fastANI
[2024-01-24 14:28:23,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg170a4326-fbd2-4a26-81c2-5b3e99188a23/GCF_900637555.1_51726_E01_genomic.fna.gz --refList GCF_900637555.1_51726_E01_genomic.fna/target_genomes.txt --output GCF_900637555.1_51726_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:40,962] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:40,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:40,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:40,979] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:40,979] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:40,979] [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
Lautropia mirabilis	strain=NCTC12852	GCA_900637555.1	47671	47671	type	True	100.0	1056	1057	95	conclusive
Lautropia mirabilis	strain=ATCC 51599	GCA_000186425.1	47671	47671	type	True	99.9751	1047	1057	95	conclusive
Lautropia dentalis	strain=KCOM 2505	GCA_003892345.1	2490857	2490857	type	True	83.9712	812	1057	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.1721	236	1057	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.0606	229	1057	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	77.7186	192	1057	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	77.6571	198	1057	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.5783	222	1057	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.5687	164	1057	95	below_threshold
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	77.457	213	1057	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	77.4543	254	1057	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	77.4466	235	1057	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	77.4161	169	1057	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	77.3322	230	1057	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	77.2714	289	1057	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	77.229	245	1057	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.21	191	1057	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	77.06	198	1057	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	76.8764	203	1057	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.4584	209	1057	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:40,981] [INFO] DFAST Taxonomy check result was written to GCF_900637555.1_51726_E01_genomic.fna/tc_result.tsv
[2024-01-24 14:28:40,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:40,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:40,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference/checkm_data
[2024-01-24 14:28:40,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:41,019] [INFO] Task started: CheckM
[2024-01-24 14:28:41,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637555.1_51726_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637555.1_51726_E01_genomic.fna/checkm_input GCF_900637555.1_51726_E01_genomic.fna/checkm_result
[2024-01-24 14:29:35,616] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:35,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:35,636] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:35,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:35,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637555.1_51726_E01_genomic.fna/markers.fasta)
[2024-01-24 14:29:35,638] [INFO] Task started: Blastn
[2024-01-24 14:29:35,638] [INFO] Running command: blastn -query GCF_900637555.1_51726_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg227114aa-b5a3-48d5-887c-8e1ae006ba7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637555.1_51726_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:37,433] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:37,436] [INFO] Selected 19 target genomes.
[2024-01-24 14:29:37,437] [INFO] Target genome list was writen to GCF_900637555.1_51726_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:37,488] [INFO] Task started: fastANI
[2024-01-24 14:29:37,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg170a4326-fbd2-4a26-81c2-5b3e99188a23/GCF_900637555.1_51726_E01_genomic.fna.gz --refList GCF_900637555.1_51726_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637555.1_51726_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:52,558] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:52,574] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:52,574] [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_900637555.1	s__Lautropia mirabilis	100.0	1056	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	97.31	96.25	0.97	0.95	6	conclusive
GCF_003892345.1	s__Lautropia dentalis	84.0064	809	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	98.32	98.32	0.98	0.98	2	-
GCA_001724315.1	s__SCN-69-89 sp001724315	78.0428	187	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970865.1	s__CAIZPE01 sp018970865	77.914	227	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307915.1	s__SCN-69-89 sp017307915	77.8432	193	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710525.1	s__CAIZPE01 sp016710525	77.8353	212	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513675.1	s__Lautropia sp012513675	77.7786	211	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002188465.1	s__Pigmentiphaga sp002188465	77.7589	194	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577305.1	s__SCN-69-89 sp003577305	77.6961	184	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.77	99.54	0.93	0.87	4	-
GCA_001724855.1	s__SCN-69-89 sp001724855	77.6277	221	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016127315.1	s__Achromobacter insuavis_A	77.6223	265	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCA_003818495.1	s__UBA4615 sp003818495	77.5839	234	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424545.1	s__Ramlibacter sp001424545	77.5422	235	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	77.5224	232	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	77.5113	168	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379565.1	s__Cupriavidus sp000379565	77.4478	238	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576795.1	s__SCN-69-89 sp003576795	77.3512	161	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898725.1	s__UBA4615 sp903898725	77.3082	201	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813615.1	s__Lautropia sp013813615	77.2931	157	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:52,576] [INFO] GTDB search result was written to GCF_900637555.1_51726_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:52,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:52,582] [INFO] DFAST_QC result json was written to GCF_900637555.1_51726_E01_genomic.fna/dqc_result.json
[2024-01-24 14:29:52,582] [INFO] DFAST_QC completed!
[2024-01-24 14:29:52,582] [INFO] Total running time: 0h1m44s