[2024-01-24 12:42:09,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference
[2024-01-24 12:42:10,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,936] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,936] [INFO] Running command: gunzip -c /var/lib/cwl/stga481259c-5c97-4ef2-9b7c-82fb69c844bf/GCF_008369935.1_ASM836993v1_genomic.fna.gz | prodigal -d GCF_008369935.1_ASM836993v1_genomic.fna/cds.fna -a GCF_008369935.1_ASM836993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:44,264] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:44,265] [INFO] Task started: HMMsearch
[2024-01-24 12:42:44,265] [INFO] Running command: hmmsearch --tblout GCF_008369935.1_ASM836993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference/reference_markers.hmm GCF_008369935.1_ASM836993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:44,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:44,663] [INFO] Found 6/6 markers.
[2024-01-24 12:42:44,738] [INFO] Query marker FASTA was written to GCF_008369935.1_ASM836993v1_genomic.fna/markers.fasta
[2024-01-24 12:42:44,739] [INFO] Task started: Blastn
[2024-01-24 12:42:44,739] [INFO] Running command: blastn -query GCF_008369935.1_ASM836993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference/reference_markers.fasta -out GCF_008369935.1_ASM836993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:45,750] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:45,754] [INFO] Selected 13 target genomes.
[2024-01-24 12:42:45,755] [INFO] Target genome list was writen to GCF_008369935.1_ASM836993v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:45,761] [INFO] Task started: fastANI
[2024-01-24 12:42:45,761] [INFO] Running command: fastANI --query /var/lib/cwl/stga481259c-5c97-4ef2-9b7c-82fb69c844bf/GCF_008369935.1_ASM836993v1_genomic.fna.gz --refList GCF_008369935.1_ASM836993v1_genomic.fna/target_genomes.txt --output GCF_008369935.1_ASM836993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:43:12,302] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:12,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:43:12,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:43:12,314] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:43:12,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:43:12,314] [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 panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	100.0	3560	3565	95	conclusive
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	89.3993	1826	3565	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	89.3083	1706	3565	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	88.3731	1848	3565	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	87.9554	1618	3565	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	86.9963	1668	3565	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	86.946	1656	3565	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	86.7547	1771	3565	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	85.9976	1804	3565	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	85.9742	1678	3565	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	85.6919	1723	3565	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	85.2908	1736	3565	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.394	1360	3565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:43:12,316] [INFO] DFAST Taxonomy check result was written to GCF_008369935.1_ASM836993v1_genomic.fna/tc_result.tsv
[2024-01-24 12:43:12,317] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:43:12,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:43:12,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference/checkm_data
[2024-01-24 12:43:12,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:43:12,417] [INFO] Task started: CheckM
[2024-01-24 12:43:12,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008369935.1_ASM836993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008369935.1_ASM836993v1_genomic.fna/checkm_input GCF_008369935.1_ASM836993v1_genomic.fna/checkm_result
[2024-01-24 12:44:42,686] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:42,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:42,718] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:42,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:42,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008369935.1_ASM836993v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:42,719] [INFO] Task started: Blastn
[2024-01-24 12:44:42,720] [INFO] Running command: blastn -query GCF_008369935.1_ASM836993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg011b9e21-53dc-4a71-a5d6-7e7b5fb4a902/dqc_reference/reference_markers_gtdb.fasta -out GCF_008369935.1_ASM836993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:44,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:44,673] [INFO] Selected 10 target genomes.
[2024-01-24 12:44:44,674] [INFO] Target genome list was writen to GCF_008369935.1_ASM836993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:44,733] [INFO] Task started: fastANI
[2024-01-24 12:44:44,734] [INFO] Running command: fastANI --query /var/lib/cwl/stga481259c-5c97-4ef2-9b7c-82fb69c844bf/GCF_008369935.1_ASM836993v1_genomic.fna.gz --refList GCF_008369935.1_ASM836993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008369935.1_ASM836993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:06,015] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:06,030] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:06,030] [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_008369935.1	s__Paraburkholderia panacisoli	100.0	3560	3565	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_902859915.1	s__Paraburkholderia ultramafica	89.4275	1822	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	89.3171	1705	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012275575.1	s__Paraburkholderia sp012275575	88.5873	1641	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859935.1	s__Paraburkholderia fynbosensis	88.3881	1846	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.83	96.83	0.79	0.79	2	-
GCF_900019265.1	s__Paraburkholderia ribeironis	87.9641	1616	3565	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	87.0777	2011	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013645.1	s__Paraburkholderia xenovorans	86.9563	1655	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	86.7437	1772	3565	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	86.6523	1739	3565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:06,032] [INFO] GTDB search result was written to GCF_008369935.1_ASM836993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:06,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:06,036] [INFO] DFAST_QC result json was written to GCF_008369935.1_ASM836993v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:06,036] [INFO] DFAST_QC completed!
[2024-01-24 12:45:06,036] [INFO] Total running time: 0h2m56s