[2024-01-24 14:40:02,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference
[2024-01-24 14:40:04,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:04,153] [INFO] Task started: Prodigal
[2024-01-24 14:40:04,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg20daca34-72c8-4f39-9624-1735e6717c70/GCF_008802135.1_ASM880213v1_genomic.fna.gz | prodigal -d GCF_008802135.1_ASM880213v1_genomic.fna/cds.fna -a GCF_008802135.1_ASM880213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:24,843] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:24,844] [INFO] Task started: HMMsearch
[2024-01-24 14:40:24,844] [INFO] Running command: hmmsearch --tblout GCF_008802135.1_ASM880213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference/reference_markers.hmm GCF_008802135.1_ASM880213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:25,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:25,181] [INFO] Found 6/6 markers.
[2024-01-24 14:40:25,236] [INFO] Query marker FASTA was written to GCF_008802135.1_ASM880213v1_genomic.fna/markers.fasta
[2024-01-24 14:40:25,237] [INFO] Task started: Blastn
[2024-01-24 14:40:25,237] [INFO] Running command: blastn -query GCF_008802135.1_ASM880213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference/reference_markers.fasta -out GCF_008802135.1_ASM880213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:26,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:26,287] [INFO] Selected 18 target genomes.
[2024-01-24 14:40:26,287] [INFO] Target genome list was writen to GCF_008802135.1_ASM880213v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:26,295] [INFO] Task started: fastANI
[2024-01-24 14:40:26,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg20daca34-72c8-4f39-9624-1735e6717c70/GCF_008802135.1_ASM880213v1_genomic.fna.gz --refList GCF_008802135.1_ASM880213v1_genomic.fna/target_genomes.txt --output GCF_008802135.1_ASM880213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:41:02,692] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:02,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:41:02,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:41:02,712] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:41:02,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:41:02,712] [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
Burkholderia latens	strain=CCUG 54555	GCA_008802135.1	488446	488446	suspected-type	True	100.0	2219	2230	95	conclusive
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	99.9925	2196	2230	95	conclusive
Burkholderia ambifaria	strain=AMMD	GCA_000203915.1	152480	152480	type	True	91.881	1781	2230	95	below_threshold
Burkholderia ambifaria	strain=AMMD	GCA_000959545.1	152480	152480	type	True	91.878	1785	2230	95	below_threshold
Burkholderia territorii		GCA_902499035.1	1503055	1503055	type	True	91.5941	1692	2230	95	below_threshold
Burkholderia territorii	strain=LMG 28158	GCA_902833055.1	1503055	1503055	type	True	91.5714	1714	2230	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	91.26	1659	2230	95	below_threshold
Burkholderia territorii	strain=CCUG 65687	GCA_008802115.1	1503055	1503055	type	True	91.0925	1199	2230	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	90.6968	1723	2230	95	below_threshold
Burkholderia pyrrocinia	strain=LMG 14191	GCA_902832895.1	60550	60550	suspected-type	True	90.4854	1709	2230	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	90.4591	1719	2230	95	below_threshold
Burkholderia vietnamiensis	strain=LMG 10929	GCA_000959445.1	60552	60552	type	True	90.4036	1606	2230	95	below_threshold
Burkholderia vietnamiensis	strain=LMG 10929	GCA_902830295.1	60552	60552	type	True	90.3989	1592	2230	95	below_threshold
Burkholderia vietnamiensis	strain=FDAARGOS_1488	GCA_020099355.1	60552	60552	type	True	90.3888	1601	2230	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	88.3677	1556	2230	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	88.3067	1596	2230	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.3743	1288	2230	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.6637	1068	2230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:41:02,714] [INFO] DFAST Taxonomy check result was written to GCF_008802135.1_ASM880213v1_genomic.fna/tc_result.tsv
[2024-01-24 14:41:02,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:41:02,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:41:02,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference/checkm_data
[2024-01-24 14:41:02,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:41:02,788] [INFO] Task started: CheckM
[2024-01-24 14:41:02,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802135.1_ASM880213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802135.1_ASM880213v1_genomic.fna/checkm_input GCF_008802135.1_ASM880213v1_genomic.fna/checkm_result
[2024-01-24 14:42:06,577] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:06,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:06,604] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:06,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:06,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802135.1_ASM880213v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:06,605] [INFO] Task started: Blastn
[2024-01-24 14:42:06,605] [INFO] Running command: blastn -query GCF_008802135.1_ASM880213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5edaf969-bbb5-4fca-9e2e-64884fdd29be/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802135.1_ASM880213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:08,784] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:08,788] [INFO] Selected 12 target genomes.
[2024-01-24 14:42:08,788] [INFO] Target genome list was writen to GCF_008802135.1_ASM880213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:08,801] [INFO] Task started: fastANI
[2024-01-24 14:42:08,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg20daca34-72c8-4f39-9624-1735e6717c70/GCF_008802135.1_ASM880213v1_genomic.fna.gz --refList GCF_008802135.1_ASM880213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802135.1_ASM880213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:34,043] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:34,058] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:34,058] [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_902499045.1	s__Burkholderia latens	99.9925	2196	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.69	99.09	0.97	0.92	4	conclusive
GCF_001718795.1	s__Burkholderia latens_A	92.8607	1753	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.33	99.18	0.94	0.92	8	-
GCF_003853415.1	s__Burkholderia sp003853415	92.2057	1739	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.32	99.32	0.91	0.91	2	-
GCF_000949135.2	s__Burkholderia sp000949135	92.1893	1751	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.23	98.18	0.87	0.85	15	-
GCF_003853645.1	s__Burkholderia sp003853645	91.9348	1711	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.08	96.08	0.79	0.79	2	-
GCF_000292915.1	s__Burkholderia cepacia_D	91.9004	1542	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203915.1	s__Burkholderia ambifaria	91.8907	1780	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.41	95.73	0.89	0.79	83	-
GCF_001443045.1	s__Burkholderia ambifaria_A	91.7086	1708	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.26	99.26	0.91	0.91	2	-
GCF_902833055.1	s__Burkholderia territorii	91.607	1710	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.1139	98.56	96.71	0.92	0.86	37	-
GCF_001718315.1	s__Burkholderia diffusa_B	91.4991	1718	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.1139	98.43	98.33	0.91	0.89	12	-
GCF_902833145.1	s__Burkholderia sp902833145	90.9699	1742	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900446215.1	s__Burkholderia cenocepacia	90.6824	1725	2230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.1666	99.08	98.68	0.89	0.81	292	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:34,061] [INFO] GTDB search result was written to GCF_008802135.1_ASM880213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:34,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:34,067] [INFO] DFAST_QC result json was written to GCF_008802135.1_ASM880213v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:34,067] [INFO] DFAST_QC completed!
[2024-01-24 14:42:34,067] [INFO] Total running time: 0h2m31s