[2024-01-24 13:13:23,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference
[2024-01-24 13:13:24,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:24,893] [INFO] Task started: Prodigal
[2024-01-24 13:13:24,893] [INFO] Running command: gunzip -c /var/lib/cwl/stga674defe-3f21-4a64-8c41-f2235319e28e/GCF_014652435.1_ASM1465243v1_genomic.fna.gz | prodigal -d GCF_014652435.1_ASM1465243v1_genomic.fna/cds.fna -a GCF_014652435.1_ASM1465243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:37,670] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:37,671] [INFO] Task started: HMMsearch
[2024-01-24 13:13:37,671] [INFO] Running command: hmmsearch --tblout GCF_014652435.1_ASM1465243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference/reference_markers.hmm GCF_014652435.1_ASM1465243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:38,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:38,096] [INFO] Found 6/6 markers.
[2024-01-24 13:13:38,187] [INFO] Query marker FASTA was written to GCF_014652435.1_ASM1465243v1_genomic.fna/markers.fasta
[2024-01-24 13:13:38,187] [INFO] Task started: Blastn
[2024-01-24 13:13:38,187] [INFO] Running command: blastn -query GCF_014652435.1_ASM1465243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference/reference_markers.fasta -out GCF_014652435.1_ASM1465243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:38,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:38,982] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:38,982] [INFO] Target genome list was writen to GCF_014652435.1_ASM1465243v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:39,007] [INFO] Task started: fastANI
[2024-01-24 13:13:39,007] [INFO] Running command: fastANI --query /var/lib/cwl/stga674defe-3f21-4a64-8c41-f2235319e28e/GCF_014652435.1_ASM1465243v1_genomic.fna.gz --refList GCF_014652435.1_ASM1465243v1_genomic.fna/target_genomes.txt --output GCF_014652435.1_ASM1465243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:52,528] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:52,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:52,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:52,540] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:52,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:52,540] [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
Undibacterium squillarum	strain=KCTC 23917	GCA_014652435.1	1131567	1131567	type	True	100.0	1385	1385	95	conclusive
Undibacterium luofuense	strain=LFS511W	GCA_018139685.1	2828733	2828733	type	True	88.5937	1204	1385	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	78.5311	448	1385	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	78.372	430	1385	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	78.3665	356	1385	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	78.3332	404	1385	95	below_threshold
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	78.2568	322	1385	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	77.2988	285	1385	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	76.3717	136	1385	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.3639	122	1385	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	76.3444	103	1385	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	76.1193	100	1385	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.1163	132	1385	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	76.0861	97	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:52,542] [INFO] DFAST Taxonomy check result was written to GCF_014652435.1_ASM1465243v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:52,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:52,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:52,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference/checkm_data
[2024-01-24 13:13:52,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:52,591] [INFO] Task started: CheckM
[2024-01-24 13:13:52,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652435.1_ASM1465243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652435.1_ASM1465243v1_genomic.fna/checkm_input GCF_014652435.1_ASM1465243v1_genomic.fna/checkm_result
[2024-01-24 13:14:33,484] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:33,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:33,528] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:33,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:33,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652435.1_ASM1465243v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:33,529] [INFO] Task started: Blastn
[2024-01-24 13:14:33,529] [INFO] Running command: blastn -query GCF_014652435.1_ASM1465243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d0961c-9fb0-4f8a-93e6-d76227f669a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652435.1_ASM1465243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:34,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:34,846] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:34,846] [INFO] Target genome list was writen to GCF_014652435.1_ASM1465243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:34,856] [INFO] Task started: fastANI
[2024-01-24 13:14:34,856] [INFO] Running command: fastANI --query /var/lib/cwl/stga674defe-3f21-4a64-8c41-f2235319e28e/GCF_014652435.1_ASM1465243v1_genomic.fna.gz --refList GCF_014652435.1_ASM1465243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652435.1_ASM1465243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:46,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:46,886] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:46,887] [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_014652435.1	s__Undibacterium squillarum	100.0	1385	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139685.1	s__Undibacterium sp018139685	88.5914	1204	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010078235.1	s__Undibacterium crateris	78.5311	448	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284235.1	s__Undibacterium sp014284235	78.3901	428	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284195.1	s__Undibacterium sp014284195	78.3665	356	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284365.1	s__Undibacterium sp014284365	78.3423	403	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014699135.1	s__Undibacterium aquatile	78.0508	338	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
GCA_016196925.1	s__Undibacterium sp016196925	77.5668	247	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284125.1	s__Undibacterium sp014284125	77.3009	285	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591035.1	s__Noviherbaspirillum sp003591035	76.3717	136	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590875.1	s__Noviherbaspirillum sp003590875	76.3639	122	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719535.1	s__Massilia aurea_A	76.2177	75	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.87	95.87	0.88	0.88	2	-
GCF_001425265.1	s__Pseudoduganella sp001425265	76.1129	124	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:46,889] [INFO] GTDB search result was written to GCF_014652435.1_ASM1465243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:46,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:46,893] [INFO] DFAST_QC result json was written to GCF_014652435.1_ASM1465243v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:46,893] [INFO] DFAST_QC completed!
[2024-01-24 13:14:46,893] [INFO] Total running time: 0h1m23s