[2023-06-13 13:31:38,856] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:31:38,861] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:31:38,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference
[2023-06-13 13:31:40,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:31:40,282] [INFO] Task started: Prodigal
[2023-06-13 13:31:40,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg64bdb73f-39cf-498f-9610-a32172150eba/GCA_947468705.1_RH-15aug16-302_genomic.fna.gz | prodigal -d GCA_947468705.1_RH-15aug16-302_genomic.fna/cds.fna -a GCA_947468705.1_RH-15aug16-302_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:31:50,927] [INFO] Task succeeded: Prodigal
[2023-06-13 13:31:50,927] [INFO] Task started: HMMsearch
[2023-06-13 13:31:50,928] [INFO] Running command: hmmsearch --tblout GCA_947468705.1_RH-15aug16-302_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference/reference_markers.hmm GCA_947468705.1_RH-15aug16-302_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:31:51,255] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:31:51,257] [INFO] Found 6/6 markers.
[2023-06-13 13:31:51,289] [INFO] Query marker FASTA was written to GCA_947468705.1_RH-15aug16-302_genomic.fna/markers.fasta
[2023-06-13 13:31:51,290] [INFO] Task started: Blastn
[2023-06-13 13:31:51,290] [INFO] Running command: blastn -query GCA_947468705.1_RH-15aug16-302_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference/reference_markers.fasta -out GCA_947468705.1_RH-15aug16-302_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:31:52,282] [INFO] Task succeeded: Blastn
[2023-06-13 13:31:52,287] [INFO] Selected 28 target genomes.
[2023-06-13 13:31:52,287] [INFO] Target genome list was writen to GCA_947468705.1_RH-15aug16-302_genomic.fna/target_genomes.txt
[2023-06-13 13:31:52,292] [INFO] Task started: fastANI
[2023-06-13 13:31:52,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg64bdb73f-39cf-498f-9610-a32172150eba/GCA_947468705.1_RH-15aug16-302_genomic.fna.gz --refList GCA_947468705.1_RH-15aug16-302_genomic.fna/target_genomes.txt --output GCA_947468705.1_RH-15aug16-302_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:32:12,378] [INFO] Task succeeded: fastANI
[2023-06-13 13:32:12,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:32:12,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:32:12,401] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:32:12,401] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:32:12,401] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.2317	162	1039	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.2157	163	1039	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.1048	149	1039	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	76.9989	175	1039	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	76.9306	166	1039	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.8873	144	1039	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.7622	167	1039	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.7153	150	1039	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	76.6437	146	1039	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.6352	129	1039	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	76.6255	151	1039	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.6229	143	1039	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.5853	135	1039	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.5728	93	1039	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.5695	132	1039	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	76.4342	179	1039	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	76.3721	171	1039	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	76.3127	137	1039	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	76.2387	144	1039	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	76.1907	107	1039	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	76.1677	127	1039	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.1612	105	1039	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	76.1171	158	1039	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	76.0041	98	1039	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	75.9772	68	1039	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	75.7564	106	1039	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	75.6865	109	1039	95	below_threshold
Paraburkholderia dinghuensis	strain=DHOA04	GCA_003837865.1	2305225	2305225	type	True	75.5558	89	1039	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:32:12,404] [INFO] DFAST Taxonomy check result was written to GCA_947468705.1_RH-15aug16-302_genomic.fna/tc_result.tsv
[2023-06-13 13:32:12,405] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:32:12,405] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:32:12,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference/checkm_data
[2023-06-13 13:32:12,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:32:12,454] [INFO] Task started: CheckM
[2023-06-13 13:32:12,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947468705.1_RH-15aug16-302_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947468705.1_RH-15aug16-302_genomic.fna/checkm_input GCA_947468705.1_RH-15aug16-302_genomic.fna/checkm_result
[2023-06-13 13:32:45,661] [INFO] Task succeeded: CheckM
[2023-06-13 13:32:45,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:32:45,691] [INFO] ===== Completeness check finished =====
[2023-06-13 13:32:45,691] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:32:45,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947468705.1_RH-15aug16-302_genomic.fna/markers.fasta)
[2023-06-13 13:32:45,692] [INFO] Task started: Blastn
[2023-06-13 13:32:45,692] [INFO] Running command: blastn -query GCA_947468705.1_RH-15aug16-302_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00afe57-9d15-4bcf-91f2-73fa7b88bdb4/dqc_reference/reference_markers_gtdb.fasta -out GCA_947468705.1_RH-15aug16-302_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:32:47,327] [INFO] Task succeeded: Blastn
[2023-06-13 13:32:47,332] [INFO] Selected 26 target genomes.
[2023-06-13 13:32:47,333] [INFO] Target genome list was writen to GCA_947468705.1_RH-15aug16-302_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:32:47,344] [INFO] Task started: fastANI
[2023-06-13 13:32:47,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg64bdb73f-39cf-498f-9610-a32172150eba/GCA_947468705.1_RH-15aug16-302_genomic.fna.gz --refList GCA_947468705.1_RH-15aug16-302_genomic.fna/target_genomes_gtdb.txt --output GCA_947468705.1_RH-15aug16-302_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:33:04,377] [INFO] Task succeeded: fastANI
[2023-06-13 13:33:04,400] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:33:04,400] [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
GCA_903895005.1	s__CAITSH01 sp903895005	80.9404	527	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAITSH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234705.1	s__2-12-FULL-64-23 sp016234705	77.6997	230	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298385.1	s__2-12-FULL-64-23 sp004298385	77.6642	214	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860395.1	s__2-12-FULL-64-23 sp014860395	77.5722	200	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860445.1	s__2-12-FULL-64-23 sp014860445	77.5476	208	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868105.1	s__RBG-16-66-20 sp016868105	77.466	165	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__RBG-16-66-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860355.1	s__2-12-FULL-64-23 sp014860355	77.3402	223	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867955.1	s__CAIYPG01 sp016867955	77.2009	109	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAIYPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649475.1	s__2-12-FULL-64-23 sp016649475	77.1363	157	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928055.1	s__CAIYPG01 sp903928055	77.0185	161	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAIYPG01	95.0	99.93	99.93	0.95	0.95	3	-
GCA_018240785.1	s__Thauera sp018240785	77.0098	136	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016189945.1	s__JACQTO01 sp016189945	76.9558	127	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JACQTO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000272025.2	s__AKCV01 sp000272025	76.7994	106	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AKCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	76.7755	165	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114795.1	s__Paucimonas sp004114795	76.6604	102	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377645.1	s__Thiomonas sp000377645	76.544	128	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	96.94	96.87	0.91	0.90	3	-
GCF_003590835.1	s__Paucimonas sp003590835	76.5283	113	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889565.1	s__PALSA-1004 sp903889565	76.4195	187	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__PALSA-1004	95.0	99.70	99.55	0.96	0.93	17	-
GCA_902825845.1	s__UBA5216 sp902825845	76.3997	122	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177795.1	s__Gallionella sp016177795	76.2767	51	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304945.1	s__Collimonas sp018304945	76.1934	107	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_009720825.1	s__Duganella radicis	76.1069	159	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913965.1	s__PALSA-1004 sp903913965	75.9316	96	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__PALSA-1004	95.0	98.84	98.17	0.81	0.70	5	-
GCA_009885185.1	s__UBA5216 sp009885185	75.3403	77	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:33:04,403] [INFO] GTDB search result was written to GCA_947468705.1_RH-15aug16-302_genomic.fna/result_gtdb.tsv
[2023-06-13 13:33:04,404] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:33:04,410] [INFO] DFAST_QC result json was written to GCA_947468705.1_RH-15aug16-302_genomic.fna/dqc_result.json
[2023-06-13 13:33:04,411] [INFO] DFAST_QC completed!
[2023-06-13 13:33:04,411] [INFO] Total running time: 0h1m26s