[2024-01-24 13:40:55,134] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference
[2024-01-24 13:40:56,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,513] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg790c8607-5d46-41e5-8a1d-e57cff304651/GCF_003269035.1_ASM326903v1_genomic.fna.gz | prodigal -d GCF_003269035.1_ASM326903v1_genomic.fna/cds.fna -a GCF_003269035.1_ASM326903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:23,396] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:23,396] [INFO] Task started: HMMsearch
[2024-01-24 13:41:23,396] [INFO] Running command: hmmsearch --tblout GCF_003269035.1_ASM326903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference/reference_markers.hmm GCF_003269035.1_ASM326903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:23,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:23,824] [INFO] Found 6/6 markers.
[2024-01-24 13:41:23,887] [INFO] Query marker FASTA was written to GCF_003269035.1_ASM326903v1_genomic.fna/markers.fasta
[2024-01-24 13:41:23,887] [INFO] Task started: Blastn
[2024-01-24 13:41:23,887] [INFO] Running command: blastn -query GCF_003269035.1_ASM326903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference/reference_markers.fasta -out GCF_003269035.1_ASM326903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:24,901] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:24,904] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:24,905] [INFO] Target genome list was writen to GCF_003269035.1_ASM326903v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:24,914] [INFO] Task started: fastANI
[2024-01-24 13:41:24,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg790c8607-5d46-41e5-8a1d-e57cff304651/GCF_003269035.1_ASM326903v1_genomic.fna.gz --refList GCF_003269035.1_ASM326903v1_genomic.fna/target_genomes.txt --output GCF_003269035.1_ASM326903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:07,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:07,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:07,286] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:07,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:07,286] [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 bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	100.0	2619	2622	95	conclusive
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.1563	1498	2622	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	87.0569	1776	2622	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	87.0442	1748	2622	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	86.9363	1554	2622	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	86.8372	1682	2622	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	86.8348	1667	2622	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	86.6817	1712	2622	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	86.4826	1608	2622	95	below_threshold
Paraburkholderia ginsengiterrae	strain=DCY85	GCA_001645125.1	1462993	1462993	type	True	86.3997	1642	2622	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	86.2722	1589	2622	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.2198	1786	2622	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	86.2068	1770	2622	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.145	1648	2622	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	86.1021	1776	2622	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.0973	1700	2622	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	86.0573	1379	2622	95	below_threshold
Paraburkholderia metrosideri	strain=LMG 28140	GCA_904848625.1	580937	580937	type	True	85.4938	1536	2622	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.5286	1184	2622	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.5211	1366	2622	95	below_threshold
Paraburkholderia atlantica	strain=CNPSo 3155	GCA_009362785.1	2654982	2654982	type	True	84.4137	1441	2622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,288] [INFO] DFAST Taxonomy check result was written to GCF_003269035.1_ASM326903v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:07,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:07,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:07,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference/checkm_data
[2024-01-24 13:42:07,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:07,371] [INFO] Task started: CheckM
[2024-01-24 13:42:07,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003269035.1_ASM326903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003269035.1_ASM326903v1_genomic.fna/checkm_input GCF_003269035.1_ASM326903v1_genomic.fna/checkm_result
[2024-01-24 13:43:16,144] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:16,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:16,179] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:16,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:16,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003269035.1_ASM326903v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:16,180] [INFO] Task started: Blastn
[2024-01-24 13:43:16,180] [INFO] Running command: blastn -query GCF_003269035.1_ASM326903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca0c330-44cc-4c3e-a7d5-77ce138042a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003269035.1_ASM326903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:17,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:17,979] [INFO] Selected 12 target genomes.
[2024-01-24 13:43:17,979] [INFO] Target genome list was writen to GCF_003269035.1_ASM326903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:18,049] [INFO] Task started: fastANI
[2024-01-24 13:43:18,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg790c8607-5d46-41e5-8a1d-e57cff304651/GCF_003269035.1_ASM326903v1_genomic.fna.gz --refList GCF_003269035.1_ASM326903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003269035.1_ASM326903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:42,288] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:42,302] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:42,303] [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_003269035.1	s__Paraburkholderia bryophila	100.0	2619	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.31	96.63	0.94	0.89	3	conclusive
GCF_013409255.1	s__Paraburkholderia sp000745015	93.2971	2205	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.63	95.38	0.90	0.84	6	-
GCF_002973525.1	s__Paraburkholderia sp002973525	92.5794	2180	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339745.1	s__Paraburkholderia sp004339745	87.3173	1759	2622	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	87.1394	1500	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020125.1	s__Paraburkholderia phytofirmans	87.0548	1746	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_902459535.1	s__Paraburkholderia sp000178415	86.7651	1666	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	86.686	1711	2622	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	86.497	1607	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900996225.1	s__Paraburkholderia sp900996225	86.4947	1681	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859805.1	s__Paraburkholderia sediminicola	86.1987	1771	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848625.1	s__Paraburkholderia metrosideri	85.4869	1537	2622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:42,305] [INFO] GTDB search result was written to GCF_003269035.1_ASM326903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:42,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:42,309] [INFO] DFAST_QC result json was written to GCF_003269035.1_ASM326903v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:42,310] [INFO] DFAST_QC completed!
[2024-01-24 13:43:42,310] [INFO] Total running time: 0h2m47s