[2024-01-24 12:16:08,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference
[2024-01-24 12:16:10,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:10,141] [INFO] Task started: Prodigal
[2024-01-24 12:16:10,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg97bac2d0-ab86-429f-9b35-58084c0a020a/GCF_003350475.1_ASM335047v1_genomic.fna.gz | prodigal -d GCF_003350475.1_ASM335047v1_genomic.fna/cds.fna -a GCF_003350475.1_ASM335047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:30,192] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:30,193] [INFO] Task started: HMMsearch
[2024-01-24 12:16:30,193] [INFO] Running command: hmmsearch --tblout GCF_003350475.1_ASM335047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference/reference_markers.hmm GCF_003350475.1_ASM335047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:30,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:30,524] [INFO] Found 6/6 markers.
[2024-01-24 12:16:30,580] [INFO] Query marker FASTA was written to GCF_003350475.1_ASM335047v1_genomic.fna/markers.fasta
[2024-01-24 12:16:30,580] [INFO] Task started: Blastn
[2024-01-24 12:16:30,580] [INFO] Running command: blastn -query GCF_003350475.1_ASM335047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference/reference_markers.fasta -out GCF_003350475.1_ASM335047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:31,632] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:31,637] [INFO] Selected 26 target genomes.
[2024-01-24 12:16:31,637] [INFO] Target genome list was writen to GCF_003350475.1_ASM335047v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:31,647] [INFO] Task started: fastANI
[2024-01-24 12:16:31,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg97bac2d0-ab86-429f-9b35-58084c0a020a/GCF_003350475.1_ASM335047v1_genomic.fna.gz --refList GCF_003350475.1_ASM335047v1_genomic.fna/target_genomes.txt --output GCF_003350475.1_ASM335047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:17:02,043] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:02,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:17:02,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:17:02,069] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:17:02,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:17:02,070] [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
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	82.6416	977	1973	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	82.3341	1100	1973	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	82.3151	1152	1973	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	82.1407	1062	1973	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	81.9948	1084	1973	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	81.945	959	1973	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	81.3486	1039	1973	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.207	741	1973	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.9085	712	1973	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.6246	793	1973	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.5745	715	1973	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.4876	820	1973	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	80.4688	825	1973	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	80.3479	698	1973	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.3445	827	1973	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	80.343	847	1973	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	80.1857	752	1973	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	80.0389	801	1973	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	79.8485	730	1973	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	79.6741	518	1973	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.6066	721	1973	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.0731	671	1973	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	78.9315	631	1973	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.8454	626	1973	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.4677	569	1973	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.3291	637	1973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:17:02,072] [INFO] DFAST Taxonomy check result was written to GCF_003350475.1_ASM335047v1_genomic.fna/tc_result.tsv
[2024-01-24 12:17:02,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:17:02,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:17:02,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference/checkm_data
[2024-01-24 12:17:02,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:17:02,135] [INFO] Task started: CheckM
[2024-01-24 12:17:02,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350475.1_ASM335047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350475.1_ASM335047v1_genomic.fna/checkm_input GCF_003350475.1_ASM335047v1_genomic.fna/checkm_result
[2024-01-24 12:19:18,457] [INFO] Task succeeded: CheckM
[2024-01-24 12:19:18,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:19:18,482] [INFO] ===== Completeness check finished =====
[2024-01-24 12:19:18,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:19:18,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350475.1_ASM335047v1_genomic.fna/markers.fasta)
[2024-01-24 12:19:18,484] [INFO] Task started: Blastn
[2024-01-24 12:19:18,484] [INFO] Running command: blastn -query GCF_003350475.1_ASM335047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b25bddf-aa2e-41d2-8412-1d41892a2f59/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350475.1_ASM335047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:19:20,599] [INFO] Task succeeded: Blastn
[2024-01-24 12:19:20,606] [INFO] Selected 10 target genomes.
[2024-01-24 12:19:20,606] [INFO] Target genome list was writen to GCF_003350475.1_ASM335047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:19:20,669] [INFO] Task started: fastANI
[2024-01-24 12:19:20,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg97bac2d0-ab86-429f-9b35-58084c0a020a/GCF_003350475.1_ASM335047v1_genomic.fna.gz --refList GCF_003350475.1_ASM335047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350475.1_ASM335047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:19:36,799] [INFO] Task succeeded: fastANI
[2024-01-24 12:19:36,812] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:19:36,812] [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_003350475.1	s__Pseudacidovorax intermedius	100.0	1970	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903864295.1	s__Pseudacidovorax sp903864295	94.9153	1791	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	97.16	95.11	0.92	0.86	4	-
GCF_900156165.1	s__Pseudacidovorax sp900156165	91.7204	1528	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	90.1057	1351	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	84.1554	1184	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503065.1	s__ALPHA2B sp005503065	84.0759	1173	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745855.1	s__Xenophilus azovorans	84.0391	1104	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217005.1	s__Variovorax sp004217005	82.748	1038	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.70	99.70	0.95	0.95	2	-
GCF_016806145.1	s__Variovorax sp900115375	82.3117	1225	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCF_003269065.1	s__Acidovorax_A anthurii	80.6105	796	1973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:19:36,814] [INFO] GTDB search result was written to GCF_003350475.1_ASM335047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:19:36,814] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:19:36,819] [INFO] DFAST_QC result json was written to GCF_003350475.1_ASM335047v1_genomic.fna/dqc_result.json
[2024-01-24 12:19:36,819] [INFO] DFAST_QC completed!
[2024-01-24 12:19:36,819] [INFO] Total running time: 0h3m28s