[2024-01-24 10:47:06,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference
[2024-01-24 10:47:12,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,821] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg87b365f7-7b23-4442-85d9-9773e5f0ba11/GCF_902153245.2_JP121.v3_genomic.fna.gz | prodigal -d GCF_902153245.2_JP121.v3_genomic.fna/cds.fna -a GCF_902153245.2_JP121.v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:25,564] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:25,565] [INFO] Task started: HMMsearch
[2024-01-24 10:47:25,565] [INFO] Running command: hmmsearch --tblout GCF_902153245.2_JP121.v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference/reference_markers.hmm GCF_902153245.2_JP121.v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:25,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:25,888] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,930] [INFO] Query marker FASTA was written to GCF_902153245.2_JP121.v3_genomic.fna/markers.fasta
[2024-01-24 10:47:25,930] [INFO] Task started: Blastn
[2024-01-24 10:47:25,930] [INFO] Running command: blastn -query GCF_902153245.2_JP121.v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference/reference_markers.fasta -out GCF_902153245.2_JP121.v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:27,098] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:27,102] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:27,103] [INFO] Target genome list was writen to GCF_902153245.2_JP121.v3_genomic.fna/target_genomes.txt
[2024-01-24 10:47:27,325] [INFO] Task started: fastANI
[2024-01-24 10:47:27,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b365f7-7b23-4442-85d9-9773e5f0ba11/GCF_902153245.2_JP121.v3_genomic.fna.gz --refList GCF_902153245.2_JP121.v3_genomic.fna/target_genomes.txt --output GCF_902153245.2_JP121.v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:43,216] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:43,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:43,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:43,235] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:43,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:43,236] [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
Pseudorhizobium endolithicum	strain=JC140	GCA_902153245.3	1191678	1191678	type	True	100.0	1381	1385	95	conclusive
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	83.7015	895	1385	95	below_threshold
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	83.5616	914	1385	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	83.552	945	1385	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	83.3252	945	1385	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.1429	614	1385	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.8967	624	1385	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.8898	672	1385	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.8438	570	1385	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	79.8327	664	1385	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.7032	568	1385	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	79.5846	525	1385	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	79.4899	561	1385	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	79.2019	569	1385	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.7672	548	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:43,238] [INFO] DFAST Taxonomy check result was written to GCF_902153245.2_JP121.v3_genomic.fna/tc_result.tsv
[2024-01-24 10:47:43,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:43,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:43,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference/checkm_data
[2024-01-24 10:47:43,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:43,297] [INFO] Task started: CheckM
[2024-01-24 10:47:43,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902153245.2_JP121.v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902153245.2_JP121.v3_genomic.fna/checkm_input GCF_902153245.2_JP121.v3_genomic.fna/checkm_result
[2024-01-24 10:48:22,443] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:22,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:22,465] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:22,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:22,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902153245.2_JP121.v3_genomic.fna/markers.fasta)
[2024-01-24 10:48:22,467] [INFO] Task started: Blastn
[2024-01-24 10:48:22,467] [INFO] Running command: blastn -query GCF_902153245.2_JP121.v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg47c4eec5-76a5-4c90-b4fb-c2d910df1c30/dqc_reference/reference_markers_gtdb.fasta -out GCF_902153245.2_JP121.v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:24,680] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:24,685] [INFO] Selected 22 target genomes.
[2024-01-24 10:48:24,686] [INFO] Target genome list was writen to GCF_902153245.2_JP121.v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:24,720] [INFO] Task started: fastANI
[2024-01-24 10:48:24,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b365f7-7b23-4442-85d9-9773e5f0ba11/GCF_902153245.2_JP121.v3_genomic.fna.gz --refList GCF_902153245.2_JP121.v3_genomic.fna/target_genomes_gtdb.txt --output GCF_902153245.2_JP121.v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:48,749] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,769] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:48,770] [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_902153245.2	s__Pseudorhizobium endolithicum	100.0	1381	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	98.09	98.09	0.93	0.93	2	conclusive
GCF_902502825.2	s__Pseudorhizobium flavum	83.5315	945	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	-
GCA_000722615.1	s__Pseudorhizobium pelagicum	81.7147	906	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	97.63	97.12	0.87	0.82	8	-
GCF_900177415.1	s__Neorhizobium oryzae_A	80.9503	782	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471605.1	s__Neorhizobium sp900471605	80.4877	753	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCF_000732195.1	s__Neorhizobium vignae	80.4735	749	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005825.1	s__Neorhizobium sp001005825	80.3897	760	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017877055.1	s__Neorhizobium galegae_D	80.3796	756	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425685.1	s__Neorhizobium sp003425685	80.2949	746	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854865.1	s__Neorhizobium sp001854865	80.2253	730	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839145.1	s__Shinella sp016839145	80.1132	622	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760785.1	s__Rhizobium_A sp018760785	80.1051	671	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	79.9608	647	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_014203155.1	s__Shinella fusca	79.8885	625	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	79.8551	694	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	79.8527	661	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_900111905.1	s__Neorhizobium sp900111905	79.8352	670	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	79.6896	671	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCF_014126615.1	s__Allorhizobium thiooxidans	79.5203	562	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193025.1	s__Rhizobium sp014193025	79.418	560	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343585.1	s__Neorhizobium sp004343585	79.0981	562	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617585.1	s__Neorhizobium cerealis	78.8658	531	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,771] [INFO] GTDB search result was written to GCF_902153245.2_JP121.v3_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:48,772] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:48,778] [INFO] DFAST_QC result json was written to GCF_902153245.2_JP121.v3_genomic.fna/dqc_result.json
[2024-01-24 10:48:48,778] [INFO] DFAST_QC completed!
[2024-01-24 10:48:48,779] [INFO] Total running time: 0h1m42s