[2024-01-24 13:37:05,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference
[2024-01-24 13:37:06,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,586] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,587] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbb558cf-26fb-44ae-b11a-04f5a082558b/GCF_031453955.1_ASM3145395v1_genomic.fna.gz | prodigal -d GCF_031453955.1_ASM3145395v1_genomic.fna/cds.fna -a GCF_031453955.1_ASM3145395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:24,696] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:24,696] [INFO] Task started: HMMsearch
[2024-01-24 13:37:24,697] [INFO] Running command: hmmsearch --tblout GCF_031453955.1_ASM3145395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference/reference_markers.hmm GCF_031453955.1_ASM3145395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:25,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:25,078] [INFO] Found 6/6 markers.
[2024-01-24 13:37:25,134] [INFO] Query marker FASTA was written to GCF_031453955.1_ASM3145395v1_genomic.fna/markers.fasta
[2024-01-24 13:37:25,134] [INFO] Task started: Blastn
[2024-01-24 13:37:25,134] [INFO] Running command: blastn -query GCF_031453955.1_ASM3145395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference/reference_markers.fasta -out GCF_031453955.1_ASM3145395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:26,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:26,136] [INFO] Selected 9 target genomes.
[2024-01-24 13:37:26,137] [INFO] Target genome list was writen to GCF_031453955.1_ASM3145395v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:26,141] [INFO] Task started: fastANI
[2024-01-24 13:37:26,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb558cf-26fb-44ae-b11a-04f5a082558b/GCF_031453955.1_ASM3145395v1_genomic.fna.gz --refList GCF_031453955.1_ASM3145395v1_genomic.fna/target_genomes.txt --output GCF_031453955.1_ASM3145395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:38,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:38,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:38,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:38,266] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:38,267] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:38,267] [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
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	93.3585	1567	1906	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	85.5994	1218	1906	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	85.1512	1239	1906	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	84.8549	1146	1906	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	83.1608	980	1906	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	83.1328	980	1906	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	82.2767	908	1906	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	81.5688	862	1906	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	79.3977	648	1906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:38,268] [INFO] DFAST Taxonomy check result was written to GCF_031453955.1_ASM3145395v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:38,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:38,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:38,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference/checkm_data
[2024-01-24 13:37:38,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:38,336] [INFO] Task started: CheckM
[2024-01-24 13:37:38,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031453955.1_ASM3145395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031453955.1_ASM3145395v1_genomic.fna/checkm_input GCF_031453955.1_ASM3145395v1_genomic.fna/checkm_result
[2024-01-24 13:38:42,691] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:42,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:42,730] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:42,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:42,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031453955.1_ASM3145395v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:42,731] [INFO] Task started: Blastn
[2024-01-24 13:38:42,731] [INFO] Running command: blastn -query GCF_031453955.1_ASM3145395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cbfee51-cc88-4457-a73a-1ef50cdbe372/dqc_reference/reference_markers_gtdb.fasta -out GCF_031453955.1_ASM3145395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:44,444] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:44,447] [INFO] Selected 9 target genomes.
[2024-01-24 13:38:44,448] [INFO] Target genome list was writen to GCF_031453955.1_ASM3145395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:44,460] [INFO] Task started: fastANI
[2024-01-24 13:38:44,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb558cf-26fb-44ae-b11a-04f5a082558b/GCF_031453955.1_ASM3145395v1_genomic.fna.gz --refList GCF_031453955.1_ASM3145395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031453955.1_ASM3145395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:57,655] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:57,668] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:57,668] [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_012932745.1	s__Xanthobacter sp012932745	97.3119	1663	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	97.23	97.23	0.90	0.90	2	conclusive
GCF_000702385.1	s__Xanthobacter sp000702385	93.3843	1533	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_012275355.1	s__Xanthobacter sp012275355	91.8868	1521	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017875275.1	s__Xanthobacter flavus	91.5171	1486	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	85.3559	1178	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807805.1	s__Xanthobacter sp016807805	85.1275	1243	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871085.1	s__Xanthobacter autotrophicus_A	84.8386	1148	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667445.1	s__Xanthobacter tagetidis	83.1925	976	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000333455.1	s__Rhodopseudomonas sp000333455	77.4381	314	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:57,670] [INFO] GTDB search result was written to GCF_031453955.1_ASM3145395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:57,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:57,674] [INFO] DFAST_QC result json was written to GCF_031453955.1_ASM3145395v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:57,674] [INFO] DFAST_QC completed!
[2024-01-24 13:38:57,675] [INFO] Total running time: 0h1m52s