[2024-01-24 15:18:51,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference
[2024-01-24 15:18:54,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,594] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,595] [INFO] Running command: gunzip -c /var/lib/cwl/stg84718a43-c2bb-4aaf-bc4c-991bd44d5516/GCF_905220975.1_LMG_31837_genomic.fna.gz | prodigal -d GCF_905220975.1_LMG_31837_genomic.fna/cds.fna -a GCF_905220975.1_LMG_31837_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:19,358] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:19,359] [INFO] Task started: HMMsearch
[2024-01-24 15:19:19,359] [INFO] Running command: hmmsearch --tblout GCF_905220975.1_LMG_31837_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference/reference_markers.hmm GCF_905220975.1_LMG_31837_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:19,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:19,740] [INFO] Found 6/6 markers.
[2024-01-24 15:19:19,803] [INFO] Query marker FASTA was written to GCF_905220975.1_LMG_31837_genomic.fna/markers.fasta
[2024-01-24 15:19:19,804] [INFO] Task started: Blastn
[2024-01-24 15:19:19,804] [INFO] Running command: blastn -query GCF_905220975.1_LMG_31837_genomic.fna/markers.fasta -db /var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference/reference_markers.fasta -out GCF_905220975.1_LMG_31837_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:20,762] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:20,765] [INFO] Selected 15 target genomes.
[2024-01-24 15:19:20,765] [INFO] Target genome list was writen to GCF_905220975.1_LMG_31837_genomic.fna/target_genomes.txt
[2024-01-24 15:19:20,774] [INFO] Task started: fastANI
[2024-01-24 15:19:20,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg84718a43-c2bb-4aaf-bc4c-991bd44d5516/GCF_905220975.1_LMG_31837_genomic.fna.gz --refList GCF_905220975.1_LMG_31837_genomic.fna/target_genomes.txt --output GCF_905220975.1_LMG_31837_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:52,380] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:52,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:52,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:52,396] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:52,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:52,396] [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 haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	100.0	2563	2568	95	conclusive
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	91.6915	1922	2568	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	91.0753	1904	2568	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	90.7131	1936	2568	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	90.7023	1955	2568	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	90.568	1917	2568	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	90.418	1971	2568	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	90.1548	1937	2568	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	90.1252	1954	2568	95	below_threshold
Paraburkholderia agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	89.6434	1878	2568	95	below_threshold
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	89.3532	1806	2568	95	below_threshold
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	89.3517	1872	2568	95	below_threshold
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	89.3277	1885	2568	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.0033	1182	2568	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.9435	1388	2568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:52,398] [INFO] DFAST Taxonomy check result was written to GCF_905220975.1_LMG_31837_genomic.fna/tc_result.tsv
[2024-01-24 15:19:52,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:52,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:52,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference/checkm_data
[2024-01-24 15:19:52,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:52,475] [INFO] Task started: CheckM
[2024-01-24 15:19:52,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905220975.1_LMG_31837_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905220975.1_LMG_31837_genomic.fna/checkm_input GCF_905220975.1_LMG_31837_genomic.fna/checkm_result
[2024-01-24 15:21:00,053] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:00,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:00,080] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:00,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:00,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905220975.1_LMG_31837_genomic.fna/markers.fasta)
[2024-01-24 15:21:00,083] [INFO] Task started: Blastn
[2024-01-24 15:21:00,083] [INFO] Running command: blastn -query GCF_905220975.1_LMG_31837_genomic.fna/markers.fasta -db /var/lib/cwl/stg571340d4-08b4-48fa-9649-561e65dda976/dqc_reference/reference_markers_gtdb.fasta -out GCF_905220975.1_LMG_31837_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:01,786] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:01,791] [INFO] Selected 13 target genomes.
[2024-01-24 15:21:01,791] [INFO] Target genome list was writen to GCF_905220975.1_LMG_31837_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:01,806] [INFO] Task started: fastANI
[2024-01-24 15:21:01,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg84718a43-c2bb-4aaf-bc4c-991bd44d5516/GCF_905220975.1_LMG_31837_genomic.fna.gz --refList GCF_905220975.1_LMG_31837_genomic.fna/target_genomes_gtdb.txt --output GCF_905220975.1_LMG_31837_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:29,770] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:29,783] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:29,784] [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_905220975.1	s__Paraburkholderia sp905220975	100.0	2564	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610295.1	s__Paraburkholderia sp003610295	92.9885	1990	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	91.7069	1919	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	91.0549	1906	2568	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	90.9448	1655	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905220835.1	s__Paraburkholderia sp905220835	90.7385	1929	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_009690905.1	s__Paraburkholderia madseniana	90.7252	1934	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_013177695.1	s__Paraburkholderia sp013177695	90.5913	1913	2568	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	90.4127	1998	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_900116445.1	s__Paraburkholderia aspalathi	90.1509	1937	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_902859805.1	s__Paraburkholderia sediminicola	90.1264	1954	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902833645.1	s__Paraburkholderia fungorum	89.3505	1872	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.62	95.59	0.90	0.75	14	-
GCF_013409845.1	s__Paraburkholderia metrosideri_A	89.0223	1694	2568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:29,786] [INFO] GTDB search result was written to GCF_905220975.1_LMG_31837_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:29,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:29,790] [INFO] DFAST_QC result json was written to GCF_905220975.1_LMG_31837_genomic.fna/dqc_result.json
[2024-01-24 15:21:29,791] [INFO] DFAST_QC completed!
[2024-01-24 15:21:29,791] [INFO] Total running time: 0h2m38s