[2024-01-24 13:31:35,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference
[2024-01-24 13:31:37,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:37,013] [INFO] Task started: Prodigal
[2024-01-24 13:31:37,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c938b36-3901-44b8-9d84-037457c5dd07/GCF_004353985.1_ASM435398v1_genomic.fna.gz | prodigal -d GCF_004353985.1_ASM435398v1_genomic.fna/cds.fna -a GCF_004353985.1_ASM435398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,338] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,339] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,339] [INFO] Running command: hmmsearch --tblout GCF_004353985.1_ASM435398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference/reference_markers.hmm GCF_004353985.1_ASM435398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,778] [INFO] Found 6/6 markers.
[2024-01-24 13:31:56,835] [INFO] Query marker FASTA was written to GCF_004353985.1_ASM435398v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,836] [INFO] Task started: Blastn
[2024-01-24 13:31:56,836] [INFO] Running command: blastn -query GCF_004353985.1_ASM435398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference/reference_markers.fasta -out GCF_004353985.1_ASM435398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,684] [INFO] Selected 21 target genomes.
[2024-01-24 13:31:57,685] [INFO] Target genome list was writen to GCF_004353985.1_ASM435398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,699] [INFO] Task started: fastANI
[2024-01-24 13:31:57,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c938b36-3901-44b8-9d84-037457c5dd07/GCF_004353985.1_ASM435398v1_genomic.fna.gz --refList GCF_004353985.1_ASM435398v1_genomic.fna/target_genomes.txt --output GCF_004353985.1_ASM435398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:25,303] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:25,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:25,321] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:25,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:25,321] [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
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	82.0075	1106	2045	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	81.9492	1121	2045	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	81.7177	1161	2045	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	81.4878	1079	2045	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	81.4684	1069	2045	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	81.0961	1091	2045	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	80.9569	1071	2045	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.5061	716	2045	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.1086	924	2045	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	79.081	955	2045	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	78.9954	932	2045	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.6703	713	2045	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	78.668	751	2045	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.5388	728	2045	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	78.4312	853	2045	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.4306	694	2045	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.345	744	2045	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	75.7124	299	2045	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	75.7118	299	2045	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	75.68	170	2045	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	75.539	192	2045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,323] [INFO] DFAST Taxonomy check result was written to GCF_004353985.1_ASM435398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:25,324] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:25,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:25,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference/checkm_data
[2024-01-24 13:32:25,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:25,394] [INFO] Task started: CheckM
[2024-01-24 13:32:25,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004353985.1_ASM435398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004353985.1_ASM435398v1_genomic.fna/checkm_input GCF_004353985.1_ASM435398v1_genomic.fna/checkm_result
[2024-01-24 13:33:35,284] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:35,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,308] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:35,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:35,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004353985.1_ASM435398v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:35,309] [INFO] Task started: Blastn
[2024-01-24 13:33:35,309] [INFO] Running command: blastn -query GCF_004353985.1_ASM435398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc1b97e2-7a5a-41e3-92eb-6e80da43e56f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004353985.1_ASM435398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,683] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:36,684] [INFO] Target genome list was writen to GCF_004353985.1_ASM435398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,722] [INFO] Task started: fastANI
[2024-01-24 13:33:36,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c938b36-3901-44b8-9d84-037457c5dd07/GCF_004353985.1_ASM435398v1_genomic.fna.gz --refList GCF_004353985.1_ASM435398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004353985.1_ASM435398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:56,601] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:56,616] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:56,617] [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_004353985.1	s__Paracraurococcus ruber	100.0	2023	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	conclusive
GCF_004343615.1	s__Paracraurococcus sp004343615	84.5276	1219	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	84.0172	1260	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355005.1	s__Paracraurococcus ruber_A	83.8742	1345	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	83.7861	1256	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008360935.1	s__Siccirubricoccus phaeus	81.9694	1185	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014283215.1	s__Siccirubricoccus deserti	81.893	1130	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016775475.1	s__Belnapia sp016775475	81.7476	1156	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	81.1952	1075	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764365.1	s__Roseococcus sp014764365	78.6816	749	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070395.1	s__CLL3-39 sp012070395	75.6957	303	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744605.1	s__Sphingobium sp017744605	75.5076	127	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745115.1	s__Sphingobium sp017745115	75.4604	107	2045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:56,618] [INFO] GTDB search result was written to GCF_004353985.1_ASM435398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:56,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:56,623] [INFO] DFAST_QC result json was written to GCF_004353985.1_ASM435398v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:56,624] [INFO] DFAST_QC completed!
[2024-01-24 13:33:56,624] [INFO] Total running time: 0h2m21s