[2023-03-15 18:39:12,220] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,220] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference
[2023-03-15 18:39:13,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stge9421fc0-2b82-4a4a-bfff-1f90ff7521d0/OceanDNA-b33296.fa | prodigal -d OceanDNA-b33296/cds.fna -a OceanDNA-b33296/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:29,378] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:29,378] [INFO] Task started: HMMsearch
[2023-03-15 18:39:29,378] [INFO] Running command: hmmsearch --tblout OceanDNA-b33296/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference/reference_markers.hmm OceanDNA-b33296/protein.faa > /dev/null
[2023-03-15 18:39:29,564] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:29,565] [INFO] Found 6/6 markers.
[2023-03-15 18:39:29,580] [INFO] Query marker FASTA was written to OceanDNA-b33296/markers.fasta
[2023-03-15 18:39:29,580] [INFO] Task started: Blastn
[2023-03-15 18:39:29,580] [INFO] Running command: blastn -query OceanDNA-b33296/markers.fasta -db /var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference/reference_markers.fasta -out OceanDNA-b33296/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:30,602] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:30,603] [INFO] Selected 22 target genomes.
[2023-03-15 18:39:30,603] [INFO] Target genome list was writen to OceanDNA-b33296/target_genomes.txt
[2023-03-15 18:39:30,617] [INFO] Task started: fastANI
[2023-03-15 18:39:30,617] [INFO] Running command: fastANI --query /var/lib/cwl/stge9421fc0-2b82-4a4a-bfff-1f90ff7521d0/OceanDNA-b33296.fa --refList OceanDNA-b33296/target_genomes.txt --output OceanDNA-b33296/fastani_result.tsv --threads 1
[2023-03-15 18:39:50,975] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:50,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:50,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:50,987] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:50,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:39:50,988] [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
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	82.8003	552	802	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	82.6866	357	802	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	82.6285	491	802	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	81.3202	480	802	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.9911	465	802	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	80.9464	464	802	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	80.9059	501	802	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	80.8349	509	802	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.6427	448	802	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	80.5058	442	802	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.316	392	802	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.252	490	802	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.2145	386	802	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0844	423	802	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	80.006	441	802	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.9636	474	802	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	79.8766	378	802	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.8165	412	802	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.7684	419	802	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	79.49	376	802	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.2526	390	802	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.8778	413	802	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:39:50,988] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33296/tc_result.tsv
[2023-03-15 18:39:50,988] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:50,988] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:50,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference/checkm_data
[2023-03-15 18:39:50,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:50,992] [INFO] Task started: CheckM
[2023-03-15 18:39:50,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33296/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33296/checkm_input OceanDNA-b33296/checkm_result
[2023-03-15 18:40:37,080] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:37,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:37,083] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:37,083] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:37,083] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33296/markers.fasta)
[2023-03-15 18:40:37,085] [INFO] Task started: Blastn
[2023-03-15 18:40:37,085] [INFO] Running command: blastn -query OceanDNA-b33296/markers.fasta -db /var/lib/cwl/stg2b1dd792-169b-472c-be5a-bfbb77c1649a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33296/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:39,197] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:39,198] [INFO] Selected 21 target genomes.
[2023-03-15 18:40:39,198] [INFO] Target genome list was writen to OceanDNA-b33296/target_genomes_gtdb.txt
[2023-03-15 18:40:39,876] [INFO] Task started: fastANI
[2023-03-15 18:40:39,877] [INFO] Running command: fastANI --query /var/lib/cwl/stge9421fc0-2b82-4a4a-bfff-1f90ff7521d0/OceanDNA-b33296.fa --refList OceanDNA-b33296/target_genomes_gtdb.txt --output OceanDNA-b33296/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:59,138] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:59,150] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:40:59,150] [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_002894305.1	s__Comamonas_C sp002894305	98.7857	688	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000204645.1	s__Alicycliphilus denitrificans	83.6292	567	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCA_018241405.1	s__Alicycliphilus sp018241405	83.3698	558	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCA_018242005.1	s__Alicycliphilus sp018242005	83.0981	510	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008575.1	s__Melaminivora_A sp003008575	83.0319	564	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054745.1	s__Alicycliphilus sp018054745	83.0074	461	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.31	99.29	0.86	0.83	3	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	82.9574	556	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811175.1	s__Melaminivora_A jejuensis	82.799	551	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400995.2	s__MR-S7 sp000400995	82.7977	536	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCA_001725235.1	s__Acidovorax_C sp001725235	82.4162	541	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_000739995.1	s__Giesbergeria granuli	82.2903	479	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_000484635.1	s__Comamonas_C badia	81.9766	496	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.01	98.01	0.89	0.89	2	-
GCF_011303755.1	s__Acidovorax_C sp011303755	81.8977	448	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725255.1	s__Comamonas_C sp001725255	81.5473	476	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.57	95.76	0.95	0.89	4	-
GCA_016703145.1	s__Ottowia sp016703145	80.85	442	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCF_003269065.1	s__Acidovorax_A anthurii	80.6472	448	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	80.0653	450	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	80.0646	480	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCF_013087525.1	s__Ramlibacter sp013087525	80.011	410	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007677875.1	s__Pseudorhodoferax boronicumulans_A	79.9668	459	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681965.1	s__Ramlibacter rhizophilus	79.9135	375	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:59,150] [INFO] GTDB search result was written to OceanDNA-b33296/result_gtdb.tsv
[2023-03-15 18:40:59,150] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:59,152] [INFO] DFAST_QC result json was written to OceanDNA-b33296/dqc_result.json
[2023-03-15 18:40:59,152] [INFO] DFAST_QC completed!
[2023-03-15 18:40:59,152] [INFO] Total running time: 0h1m47s