[2024-01-24 13:31:30,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:30,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:30,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference
[2024-01-24 13:31:31,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:31,382] [INFO] Task started: Prodigal
[2024-01-24 13:31:31,382] [INFO] Running command: gunzip -c /var/lib/cwl/stgcda127e0-75ea-474a-bcb6-7ff3b7a234a5/GCF_004402975.1_ASM440297v1_genomic.fna.gz | prodigal -d GCF_004402975.1_ASM440297v1_genomic.fna/cds.fna -a GCF_004402975.1_ASM440297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:04,480] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:04,480] [INFO] Task started: HMMsearch
[2024-01-24 13:32:04,481] [INFO] Running command: hmmsearch --tblout GCF_004402975.1_ASM440297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference/reference_markers.hmm GCF_004402975.1_ASM440297v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:04,945] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:04,946] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,019] [INFO] Query marker FASTA was written to GCF_004402975.1_ASM440297v1_genomic.fna/markers.fasta
[2024-01-24 13:32:05,019] [INFO] Task started: Blastn
[2024-01-24 13:32:05,020] [INFO] Running command: blastn -query GCF_004402975.1_ASM440297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference/reference_markers.fasta -out GCF_004402975.1_ASM440297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,103] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,107] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:06,107] [INFO] Target genome list was writen to GCF_004402975.1_ASM440297v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,127] [INFO] Task started: fastANI
[2024-01-24 13:32:06,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgcda127e0-75ea-474a-bcb6-7ff3b7a234a5/GCF_004402975.1_ASM440297v1_genomic.fna.gz --refList GCF_004402975.1_ASM440297v1_genomic.fna/target_genomes.txt --output GCF_004402975.1_ASM440297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:35,625] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:35,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:35,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:35,637] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:35,637] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:35,637] [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 dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	100.0	3400	3418	95	inconclusive
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	95.8251	2256	3418	95	inconclusive
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	89.4268	1916	3418	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	89.2475	1880	3418	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	89.2473	1875	3418	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.6112	1601	3418	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.7308	1865	3418	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	86.6478	1672	3418	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	86.6284	1726	3418	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.611	1717	3418	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.5793	1798	3418	95	below_threshold
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	86.1228	1817	3418	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.7981	1374	3418	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.6824	1548	3418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:35,639] [INFO] DFAST Taxonomy check result was written to GCF_004402975.1_ASM440297v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:35,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:35,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:35,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference/checkm_data
[2024-01-24 13:32:35,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:35,734] [INFO] Task started: CheckM
[2024-01-24 13:32:35,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402975.1_ASM440297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402975.1_ASM440297v1_genomic.fna/checkm_input GCF_004402975.1_ASM440297v1_genomic.fna/checkm_result
[2024-01-24 13:34:06,369] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:06,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:06,398] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:06,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:06,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402975.1_ASM440297v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:06,399] [INFO] Task started: Blastn
[2024-01-24 13:34:06,399] [INFO] Running command: blastn -query GCF_004402975.1_ASM440297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22ea035f-8796-46d3-8052-6cf4e8157867/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402975.1_ASM440297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:08,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:08,436] [INFO] Selected 7 target genomes.
[2024-01-24 13:34:08,436] [INFO] Target genome list was writen to GCF_004402975.1_ASM440297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:08,452] [INFO] Task started: fastANI
[2024-01-24 13:34:08,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgcda127e0-75ea-474a-bcb6-7ff3b7a234a5/GCF_004402975.1_ASM440297v1_genomic.fna.gz --refList GCF_004402975.1_ASM440297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402975.1_ASM440297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:24,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:24,760] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:24,760] [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_000020125.1	s__Paraburkholderia phytofirmans	95.8044	2256	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	conclusive
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	93.0494	2219	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002025.1	s__Paraburkholderia sp003002025	92.9628	2128	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_004339745.1	s__Paraburkholderia sp004339745	91.8507	2174	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	89.4341	1916	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104795.1	s__Paraburkholderia sp900104795	89.2929	1988	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.49	98.44	0.88	0.86	5	-
GCF_000013645.1	s__Paraburkholderia xenovorans	89.2455	1871	3418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:24,762] [INFO] GTDB search result was written to GCF_004402975.1_ASM440297v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:24,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:24,768] [INFO] DFAST_QC result json was written to GCF_004402975.1_ASM440297v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:24,768] [INFO] DFAST_QC completed!
[2024-01-24 13:34:24,768] [INFO] Total running time: 0h2m55s