[2024-01-24 13:37:01,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:01,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:01,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference
[2024-01-24 13:37:03,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:03,091] [INFO] Task started: Prodigal
[2024-01-24 13:37:03,092] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ad7c4df-23eb-4b27-91dd-4f135fac0295/GCF_902833635.1_ASM90283363v1_genomic.fna.gz | prodigal -d GCF_902833635.1_ASM90283363v1_genomic.fna/cds.fna -a GCF_902833635.1_ASM90283363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:26,278] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:26,279] [INFO] Task started: HMMsearch
[2024-01-24 13:37:26,279] [INFO] Running command: hmmsearch --tblout GCF_902833635.1_ASM90283363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference/reference_markers.hmm GCF_902833635.1_ASM90283363v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:26,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:26,688] [INFO] Found 6/6 markers.
[2024-01-24 13:37:26,750] [INFO] Query marker FASTA was written to GCF_902833635.1_ASM90283363v1_genomic.fna/markers.fasta
[2024-01-24 13:37:26,751] [INFO] Task started: Blastn
[2024-01-24 13:37:26,752] [INFO] Running command: blastn -query GCF_902833635.1_ASM90283363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference/reference_markers.fasta -out GCF_902833635.1_ASM90283363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:27,815] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:27,819] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:27,820] [INFO] Target genome list was writen to GCF_902833635.1_ASM90283363v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:27,831] [INFO] Task started: fastANI
[2024-01-24 13:37:27,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ad7c4df-23eb-4b27-91dd-4f135fac0295/GCF_902833635.1_ASM90283363v1_genomic.fna.gz --refList GCF_902833635.1_ASM90283363v1_genomic.fna/target_genomes.txt --output GCF_902833635.1_ASM90283363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:50,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:50,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:50,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:50,801] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:50,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:50,801] [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 caledonica	strain=LMG 19076	GCA_902833635.1	134536	134536	type	True	100.0	2408	2412	95	conclusive
Paraburkholderia caledonica	strain=NBRC 102488	GCA_000685095.1	134536	134536	type	True	99.9812	2379	2412	95	conclusive
Paraburkholderia kirstenboschensis	strain=LMG 28727	GCA_904848585.1	1245436	1245436	type	True	93.1861	2000	2412	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	92.8661	1600	2412	95	below_threshold
Paraburkholderia dilworthii	strain=WSM3556	GCA_000472525.1	948106	948106	type	True	89.1945	1735	2412	95	below_threshold
Paraburkholderia rhynchosiae	strain=LMG 27174	GCA_902859775.1	487049	487049	type	True	87.6254	1640	2412	95	below_threshold
Paraburkholderia graminis	strain=LMG 18924	GCA_902859785.1	60548	60548	type	True	87.4532	1783	2412	95	below_threshold
Paraburkholderia graminis	strain=C4D1M	GCA_000172415.1	60548	60548	type	True	87.3365	1739	2412	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	84.2193	1398	2412	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	84.1819	1500	2412	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	84.0796	1431	2412	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.1941	1364	2412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,803] [INFO] DFAST Taxonomy check result was written to GCF_902833635.1_ASM90283363v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:50,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:50,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:50,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference/checkm_data
[2024-01-24 13:37:50,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:50,881] [INFO] Task started: CheckM
[2024-01-24 13:37:50,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833635.1_ASM90283363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833635.1_ASM90283363v1_genomic.fna/checkm_input GCF_902833635.1_ASM90283363v1_genomic.fna/checkm_result
[2024-01-24 13:38:56,083] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:56,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:56,112] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:56,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:56,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833635.1_ASM90283363v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:56,113] [INFO] Task started: Blastn
[2024-01-24 13:38:56,113] [INFO] Running command: blastn -query GCF_902833635.1_ASM90283363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bbe60ac-05c7-4190-b86c-a140bfe2f94e/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833635.1_ASM90283363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:57,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:57,973] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:57,973] [INFO] Target genome list was writen to GCF_902833635.1_ASM90283363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:57,986] [INFO] Task started: fastANI
[2024-01-24 13:38:57,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ad7c4df-23eb-4b27-91dd-4f135fac0295/GCF_902833635.1_ASM90283363v1_genomic.fna.gz --refList GCF_902833635.1_ASM90283363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833635.1_ASM90283363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:12,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:12,801] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:12,801] [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_000685095.1	s__Paraburkholderia caledonica	99.9793	2380	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.03	95.65	0.88	0.80	10	conclusive
GCF_904848585.1	s__Paraburkholderia kirstenboschensis	93.1872	2000	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000472525.1	s__Paraburkholderia dilworthii	89.1925	1735	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879865.1	s__Paraburkholderia rhynchosiae	87.6038	1660	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000172415.1	s__Paraburkholderia graminis	87.3291	1740	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.52	98.23	0.90	0.89	12	-
GCF_000472445.1	s__Paraburkholderia sp000472445	86.9263	1587	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148685.1	s__Paraburkholderia sp000148685	85.9702	1684	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.01	98.00	0.91	0.91	4	-
GCF_008369935.1	s__Paraburkholderia panacisoli	84.5733	1538	2412	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 13:39:12,805] [INFO] GTDB search result was written to GCF_902833635.1_ASM90283363v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:12,805] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:12,808] [INFO] DFAST_QC result json was written to GCF_902833635.1_ASM90283363v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:12,809] [INFO] DFAST_QC completed!
[2024-01-24 13:39:12,809] [INFO] Total running time: 0h2m11s