[2024-01-24 13:40:46,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference
[2024-01-24 13:40:47,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,417] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,418] [INFO] Running command: gunzip -c /var/lib/cwl/stge2850793-f5ab-4cd0-a786-232ed22d16be/GCF_009857475.1_ASM985747v1_genomic.fna.gz | prodigal -d GCF_009857475.1_ASM985747v1_genomic.fna/cds.fna -a GCF_009857475.1_ASM985747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,739] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,739] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,740] [INFO] Running command: hmmsearch --tblout GCF_009857475.1_ASM985747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference/reference_markers.hmm GCF_009857475.1_ASM985747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,054] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,055] [INFO] Found 6/6 markers.
[2024-01-24 13:41:06,104] [INFO] Query marker FASTA was written to GCF_009857475.1_ASM985747v1_genomic.fna/markers.fasta
[2024-01-24 13:41:06,104] [INFO] Task started: Blastn
[2024-01-24 13:41:06,104] [INFO] Running command: blastn -query GCF_009857475.1_ASM985747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference/reference_markers.fasta -out GCF_009857475.1_ASM985747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:07,034] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:07,038] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:07,039] [INFO] Target genome list was writen to GCF_009857475.1_ASM985747v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:07,046] [INFO] Task started: fastANI
[2024-01-24 13:41:07,046] [INFO] Running command: fastANI --query /var/lib/cwl/stge2850793-f5ab-4cd0-a786-232ed22d16be/GCF_009857475.1_ASM985747v1_genomic.fna.gz --refList GCF_009857475.1_ASM985747v1_genomic.fna/target_genomes.txt --output GCF_009857475.1_ASM985747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:33,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:33,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:33,122] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:33,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:33,123] [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
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	100.0	1877	1880	95	conclusive
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	82.3219	1130	1880	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	82.2675	1115	1880	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	81.9614	1131	1880	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	81.4182	1054	1880	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	81.186	1019	1880	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	81.0398	948	1880	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	80.7001	1044	1880	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	80.6959	966	1880	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	80.5563	990	1880	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	80.523	1031	1880	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	80.5113	952	1880	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	80.4998	804	1880	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	80.4169	866	1880	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.3953	875	1880	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.3111	876	1880	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	80.0621	917	1880	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.0493	829	1880	95	below_threshold
Pseudoduganella ginsengisoli	strain=KCTC 42409	GCA_009720865.1	1462440	1462440	type	True	79.7075	886	1880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,124] [INFO] DFAST Taxonomy check result was written to GCF_009857475.1_ASM985747v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:33,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:33,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:33,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference/checkm_data
[2024-01-24 13:41:33,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:33,184] [INFO] Task started: CheckM
[2024-01-24 13:41:33,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857475.1_ASM985747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857475.1_ASM985747v1_genomic.fna/checkm_input GCF_009857475.1_ASM985747v1_genomic.fna/checkm_result
[2024-01-24 13:42:24,801] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:24,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,826] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:24,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:24,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857475.1_ASM985747v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:24,827] [INFO] Task started: Blastn
[2024-01-24 13:42:24,827] [INFO] Running command: blastn -query GCF_009857475.1_ASM985747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03e3a2ba-3c47-4415-b35e-8e67852e4c45/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857475.1_ASM985747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:26,592] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:26,596] [INFO] Selected 7 target genomes.
[2024-01-24 13:42:26,596] [INFO] Target genome list was writen to GCF_009857475.1_ASM985747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:26,666] [INFO] Task started: fastANI
[2024-01-24 13:42:26,667] [INFO] Running command: fastANI --query /var/lib/cwl/stge2850793-f5ab-4cd0-a786-232ed22d16be/GCF_009857475.1_ASM985747v1_genomic.fna.gz --refList GCF_009857475.1_ASM985747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857475.1_ASM985747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:37,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:37,992] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:37,992] [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_009857475.1	s__Pseudoduganella guangdongensis	100.0	1877	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217275.1	s__Pseudoduganella sp004217275	86.4226	1419	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113115.1	s__Pseudoduganella sp900113115	86.3768	1459	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425005.1	s__Pseudoduganella sp001425005	86.2196	1467	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.68	99.68	0.97	0.97	2	-
GCF_001427305.1	s__Pseudoduganella sp001427305	86.2116	1450	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425385.1	s__Pseudoduganella violaceinigra	86.1992	1388	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720745.1	s__Pseudoduganella eburnea	86.1718	1371	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:37,994] [INFO] GTDB search result was written to GCF_009857475.1_ASM985747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:37,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:37,999] [INFO] DFAST_QC result json was written to GCF_009857475.1_ASM985747v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:37,999] [INFO] DFAST_QC completed!
[2024-01-24 13:42:37,999] [INFO] Total running time: 0h1m52s