[2024-01-25 18:39:50,745] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference
[2024-01-25 18:39:51,869] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,870] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d7376c3-54ad-4bc4-b3e2-48f7911f6119/GCF_907164575.1_LMG_32171_genomic.fna.gz | prodigal -d GCF_907164575.1_LMG_32171_genomic.fna/cds.fna -a GCF_907164575.1_LMG_32171_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:08,043] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:08,043] [INFO] Task started: HMMsearch
[2024-01-25 18:40:08,043] [INFO] Running command: hmmsearch --tblout GCF_907164575.1_LMG_32171_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference/reference_markers.hmm GCF_907164575.1_LMG_32171_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:08,364] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:08,365] [INFO] Found 6/6 markers.
[2024-01-25 18:40:08,428] [INFO] Query marker FASTA was written to GCF_907164575.1_LMG_32171_genomic.fna/markers.fasta
[2024-01-25 18:40:08,428] [INFO] Task started: Blastn
[2024-01-25 18:40:08,428] [INFO] Running command: blastn -query GCF_907164575.1_LMG_32171_genomic.fna/markers.fasta -db /var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference/reference_markers.fasta -out GCF_907164575.1_LMG_32171_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:09,358] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:09,362] [INFO] Selected 16 target genomes.
[2024-01-25 18:40:09,362] [INFO] Target genome list was writen to GCF_907164575.1_LMG_32171_genomic.fna/target_genomes.txt
[2024-01-25 18:40:09,366] [INFO] Task started: fastANI
[2024-01-25 18:40:09,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d7376c3-54ad-4bc4-b3e2-48f7911f6119/GCF_907164575.1_LMG_32171_genomic.fna.gz --refList GCF_907164575.1_LMG_32171_genomic.fna/target_genomes.txt --output GCF_907164575.1_LMG_32171_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:36,062] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:36,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:36,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:36,084] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:36,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:36,085] [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
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	100.0	1906	1910	95	conclusive
Paraburkholderia sartisoli	strain=LMG 24000	GCA_900107685.1	83784	83784	type	True	92.9667	1540	1910	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	90.1064	1483	1910	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	83.3715	1164	1910	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	83.3036	1129	1910	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	83.168	1237	1910	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	83.1142	1162	1910	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	82.9564	1177	1910	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	82.9522	1176	1910	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	82.9048	1188	1910	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	82.8895	1180	1910	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	82.8242	1132	1910	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.8175	1138	1910	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	82.6205	1207	1910	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_900109265.1	92647	92647	type	True	81.5419	1071	1910	95	below_threshold
Paraburkholderia acidisoli	strain=DHF22	GCA_009789675.1	2571748	2571748	type	True	81.3213	1030	1910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:36,087] [INFO] DFAST Taxonomy check result was written to GCF_907164575.1_LMG_32171_genomic.fna/tc_result.tsv
[2024-01-25 18:40:36,087] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:36,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:36,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference/checkm_data
[2024-01-25 18:40:36,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:36,170] [INFO] Task started: CheckM
[2024-01-25 18:40:36,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_907164575.1_LMG_32171_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_907164575.1_LMG_32171_genomic.fna/checkm_input GCF_907164575.1_LMG_32171_genomic.fna/checkm_result
[2024-01-25 18:41:24,465] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:24,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:24,497] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:24,498] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:24,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_907164575.1_LMG_32171_genomic.fna/markers.fasta)
[2024-01-25 18:41:24,498] [INFO] Task started: Blastn
[2024-01-25 18:41:24,498] [INFO] Running command: blastn -query GCF_907164575.1_LMG_32171_genomic.fna/markers.fasta -db /var/lib/cwl/stg72d2a7c7-4d73-4e2b-8d7a-cec2b49ee2df/dqc_reference/reference_markers_gtdb.fasta -out GCF_907164575.1_LMG_32171_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:26,286] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:26,289] [INFO] Selected 23 target genomes.
[2024-01-25 18:41:26,289] [INFO] Target genome list was writen to GCF_907164575.1_LMG_32171_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:26,294] [INFO] Task started: fastANI
[2024-01-25 18:41:26,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d7376c3-54ad-4bc4-b3e2-48f7911f6119/GCF_907164575.1_LMG_32171_genomic.fna.gz --refList GCF_907164575.1_LMG_32171_genomic.fna/target_genomes_gtdb.txt --output GCF_907164575.1_LMG_32171_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:06,120] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:06,134] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:42:06,134] [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_900107685.1	s__Paraburkholderia sartisoli	92.9876	1538	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.92	96.92	0.85	0.85	2	-
GCF_004361815.1	s__Paraburkholderia sp004361815	83.9753	1253	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	83.3848	1162	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177725.1	s__Paraburkholderia susongensis	83.3137	1146	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859915.1	s__Paraburkholderia ultramafica	83.3088	1128	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	83.2993	1097	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_012927125.1	s__Paraburkholderia sp012927125	83.2712	1156	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369935.1	s__Paraburkholderia panacisoli	83.1701	1237	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353175.1	s__Paraburkholderia lacunae	83.1396	1158	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931485.1	s__Paraburkholderia sp001931485	83.1043	1093	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859935.1	s__Paraburkholderia fynbosensis	83.0485	1183	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.83	96.83	0.79	0.79	2	-
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	82.9573	1260	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	82.942	1178	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	82.8954	1219	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397785.1	s__Paraburkholderia sp014397785	82.8154	1138	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177695.1	s__Paraburkholderia sp013177695	82.8052	1133	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	82.802	1087	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610295.1	s__Paraburkholderia sp003610295	82.802	1146	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	82.7986	1170	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_005503145.1	s__Paraburkholderia sp005503145	82.3399	1084	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	81.3233	1025	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789675.1	s__Paraburkholderia acidisoli	81.3052	1032	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	81.1953	1010	1910	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:06,137] [INFO] GTDB search result was written to GCF_907164575.1_LMG_32171_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:06,137] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:06,141] [INFO] DFAST_QC result json was written to GCF_907164575.1_LMG_32171_genomic.fna/dqc_result.json
[2024-01-25 18:42:06,141] [INFO] DFAST_QC completed!
[2024-01-25 18:42:06,141] [INFO] Total running time: 0h2m15s