[2024-01-24 12:36:22,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:22,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:22,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference
[2024-01-24 12:36:24,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:24,100] [INFO] Task started: Prodigal
[2024-01-24 12:36:24,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg6322dcf8-9ce6-4e66-948b-6e925bb12be1/GCF_014635325.1_ASM1463532v1_genomic.fna.gz | prodigal -d GCF_014635325.1_ASM1463532v1_genomic.fna/cds.fna -a GCF_014635325.1_ASM1463532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:45,472] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:45,472] [INFO] Task started: HMMsearch
[2024-01-24 12:36:45,473] [INFO] Running command: hmmsearch --tblout GCF_014635325.1_ASM1463532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference/reference_markers.hmm GCF_014635325.1_ASM1463532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:45,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:45,804] [INFO] Found 6/6 markers.
[2024-01-24 12:36:45,854] [INFO] Query marker FASTA was written to GCF_014635325.1_ASM1463532v1_genomic.fna/markers.fasta
[2024-01-24 12:36:45,855] [INFO] Task started: Blastn
[2024-01-24 12:36:45,855] [INFO] Running command: blastn -query GCF_014635325.1_ASM1463532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference/reference_markers.fasta -out GCF_014635325.1_ASM1463532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:46,877] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:46,883] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:46,884] [INFO] Target genome list was writen to GCF_014635325.1_ASM1463532v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:46,890] [INFO] Task started: fastANI
[2024-01-24 12:36:46,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg6322dcf8-9ce6-4e66-948b-6e925bb12be1/GCF_014635325.1_ASM1463532v1_genomic.fna.gz --refList GCF_014635325.1_ASM1463532v1_genomic.fna/target_genomes.txt --output GCF_014635325.1_ASM1463532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:03,475] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:03,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:03,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:03,490] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:03,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:03,490] [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
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	100.0	2119	2119	95	conclusive
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	84.8521	1290	2119	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	83.9544	1188	2119	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	80.8781	908	2119	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	80.8518	842	2119	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	80.7818	859	2119	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	80.7494	803	2119	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	80.452	804	2119	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	80.4325	800	2119	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	79.85	684	2119	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	79.0365	607	2119	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	79.0111	672	2119	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	78.7607	667	2119	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.7532	417	2119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:03,492] [INFO] DFAST Taxonomy check result was written to GCF_014635325.1_ASM1463532v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:03,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:03,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:03,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference/checkm_data
[2024-01-24 12:37:03,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:03,558] [INFO] Task started: CheckM
[2024-01-24 12:37:03,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635325.1_ASM1463532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635325.1_ASM1463532v1_genomic.fna/checkm_input GCF_014635325.1_ASM1463532v1_genomic.fna/checkm_result
[2024-01-24 12:38:14,264] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:14,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:14,290] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:14,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:14,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635325.1_ASM1463532v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:14,291] [INFO] Task started: Blastn
[2024-01-24 12:38:14,291] [INFO] Running command: blastn -query GCF_014635325.1_ASM1463532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16830cd0-240b-4541-9d25-520d3cfe0b25/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635325.1_ASM1463532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:15,989] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:15,993] [INFO] Selected 14 target genomes.
[2024-01-24 12:38:15,993] [INFO] Target genome list was writen to GCF_014635325.1_ASM1463532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:16,033] [INFO] Task started: fastANI
[2024-01-24 12:38:16,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg6322dcf8-9ce6-4e66-948b-6e925bb12be1/GCF_014635325.1_ASM1463532v1_genomic.fna.gz --refList GCF_014635325.1_ASM1463532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635325.1_ASM1463532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:32,205] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:32,219] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:32,219] [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_014635325.1	s__Azorhizobium oxalatiphilum	100.0	2119	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000473085.1	s__Azorhizobium doebereinerae	84.8688	1288	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010525.1	s__Azorhizobium caulinodans	83.9586	1187	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCA_013911975.1	s__Aquabacter sp013911975	81.1599	789	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932745.1	s__Xanthobacter sp012932745	81.0378	858	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	97.23	97.23	0.90	0.90	2	-
GCF_000702385.1	s__Xanthobacter sp000702385	81.0168	880	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_003993795.1	s__Aquabacter cavernae	80.9813	820	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	80.8961	812	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275355.1	s__Xanthobacter sp012275355	80.8641	850	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008364685.1	s__Xanthobacter sp008364685	80.8493	843	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742835.1	s__Aquabacter sp017742835	80.8013	856	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279855.1	s__Aquabacter sp002279855	80.6601	610	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	98.44	97.78	0.75	0.72	3	-
GCF_003667445.1	s__Xanthobacter tagetidis	80.4614	802	2119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:32,220] [INFO] GTDB search result was written to GCF_014635325.1_ASM1463532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:32,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:32,224] [INFO] DFAST_QC result json was written to GCF_014635325.1_ASM1463532v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:32,224] [INFO] DFAST_QC completed!
[2024-01-24 12:38:32,224] [INFO] Total running time: 0h2m9s