[2024-01-25 20:04:35,742] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:35,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:35,744] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference
[2024-01-25 20:04:36,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:36,918] [INFO] Task started: Prodigal
[2024-01-25 20:04:36,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg48f25f37-1bd3-43d8-b535-33ec1666ec41/GCF_904848665.1_LMG_27952_genomic.fna.gz | prodigal -d GCF_904848665.1_LMG_27952_genomic.fna/cds.fna -a GCF_904848665.1_LMG_27952_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:01,542] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:01,543] [INFO] Task started: HMMsearch
[2024-01-25 20:05:01,543] [INFO] Running command: hmmsearch --tblout GCF_904848665.1_LMG_27952_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference/reference_markers.hmm GCF_904848665.1_LMG_27952_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:01,851] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:01,852] [INFO] Found 6/6 markers.
[2024-01-25 20:05:01,913] [INFO] Query marker FASTA was written to GCF_904848665.1_LMG_27952_genomic.fna/markers.fasta
[2024-01-25 20:05:01,914] [INFO] Task started: Blastn
[2024-01-25 20:05:01,914] [INFO] Running command: blastn -query GCF_904848665.1_LMG_27952_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference/reference_markers.fasta -out GCF_904848665.1_LMG_27952_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:02,860] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:02,863] [INFO] Selected 12 target genomes.
[2024-01-25 20:05:02,863] [INFO] Target genome list was writen to GCF_904848665.1_LMG_27952_genomic.fna/target_genomes.txt
[2024-01-25 20:05:02,865] [INFO] Task started: fastANI
[2024-01-25 20:05:02,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f25f37-1bd3-43d8-b535-33ec1666ec41/GCF_904848665.1_LMG_27952_genomic.fna.gz --refList GCF_904848665.1_LMG_27952_genomic.fna/target_genomes.txt --output GCF_904848665.1_LMG_27952_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:27,998] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:27,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:27,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:28,007] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:28,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:28,008] [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 hiiakae	strain=LMG 27952	GCA_904848665.1	1081782	1081782	type	True	100.0	2874	2876	95	conclusive
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	92.9599	2143	2876	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	92.0737	2057	2876	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	91.7012	2131	2876	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	91.3657	1801	2876	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_900109265.1	92647	92647	type	True	85.107	1576	2876	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	84.9795	1770	2876	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	84.9418	1662	2876	95	below_threshold
Paraburkholderia eburnea	strain=JCM 18070	GCA_002917095.1	1189126	1189126	type	True	84.7613	1492	2876	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.026	1010	2876	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	80.9706	1198	2876	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	80.9192	1298	2876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:28,025] [INFO] DFAST Taxonomy check result was written to GCF_904848665.1_LMG_27952_genomic.fna/tc_result.tsv
[2024-01-25 20:05:28,026] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:28,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:28,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference/checkm_data
[2024-01-25 20:05:28,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:28,108] [INFO] Task started: CheckM
[2024-01-25 20:05:28,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904848665.1_LMG_27952_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904848665.1_LMG_27952_genomic.fna/checkm_input GCF_904848665.1_LMG_27952_genomic.fna/checkm_result
[2024-01-25 20:06:37,483] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:37,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:37,508] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:37,508] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:37,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904848665.1_LMG_27952_genomic.fna/markers.fasta)
[2024-01-25 20:06:37,509] [INFO] Task started: Blastn
[2024-01-25 20:06:37,509] [INFO] Running command: blastn -query GCF_904848665.1_LMG_27952_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8220253-f7ce-4eaf-97e4-efa29edbf273/dqc_reference/reference_markers_gtdb.fasta -out GCF_904848665.1_LMG_27952_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:39,439] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:39,442] [INFO] Selected 9 target genomes.
[2024-01-25 20:06:39,442] [INFO] Target genome list was writen to GCF_904848665.1_LMG_27952_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:39,447] [INFO] Task started: fastANI
[2024-01-25 20:06:39,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f25f37-1bd3-43d8-b535-33ec1666ec41/GCF_904848665.1_LMG_27952_genomic.fna.gz --refList GCF_904848665.1_LMG_27952_genomic.fna/target_genomes_gtdb.txt --output GCF_904848665.1_LMG_27952_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:58,881] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:58,889] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:58,889] [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_904848665.1	s__Paraburkholderia hiiakae	100.0	2874	2876	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_009789655.1	s__Paraburkholderia acidiphila	92.9542	2143	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519185.1	s__Paraburkholderia nodosa	92.0747	2057	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	91.7093	2130	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	91.6227	1783	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	91.5719	1960	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739775.1	s__Paraburkholderia heleia	91.373	1799	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	-
GCF_003268775.1	s__Paraburkholderia unamae	88.4848	1943	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.69	98.69	0.91	0.91	2	-
GCF_002917095.1	s__Paraburkholderia eburnea	84.77	1490	2876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.11	98.22	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:58,890] [INFO] GTDB search result was written to GCF_904848665.1_LMG_27952_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:58,891] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:58,894] [INFO] DFAST_QC result json was written to GCF_904848665.1_LMG_27952_genomic.fna/dqc_result.json
[2024-01-25 20:06:58,894] [INFO] DFAST_QC completed!
[2024-01-25 20:06:58,894] [INFO] Total running time: 0h2m23s