[2024-01-24 11:26:20,776] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,778] [INFO] DQC Reference Directory: /var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference
[2024-01-24 11:26:21,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:21,982] [INFO] Task started: Prodigal
[2024-01-24 11:26:21,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg7504c0ad-b984-48e3-9918-1ceba5a54643/GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/cds.fna -a GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:55,982] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:55,982] [INFO] Task started: HMMsearch
[2024-01-24 11:26:55,982] [INFO] Running command: hmmsearch --tblout GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference/reference_markers.hmm GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:56,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:56,503] [INFO] Found 6/6 markers.
[2024-01-24 11:26:56,586] [INFO] Query marker FASTA was written to GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:26:56,586] [INFO] Task started: Blastn
[2024-01-24 11:26:56,586] [INFO] Running command: blastn -query GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference/reference_markers.fasta -out GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:57,556] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:57,561] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:57,561] [INFO] Target genome list was writen to GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:26:57,570] [INFO] Task started: fastANI
[2024-01-24 11:26:57,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg7504c0ad-b984-48e3-9918-1ceba5a54643/GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna.gz --refList GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:27,966] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:27,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:27,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:27,982] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:27:27,983] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:27,983] [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 hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	100.0	3625	3636	95	inconclusive
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	99.9879	3591	3636	95	inconclusive
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	99.7671	3432	3636	95	inconclusive
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	95.2388	2614	3636	95	inconclusive
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	95.2071	2705	3636	95	inconclusive
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	87.9495	2301	3636	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.3698	1233	3636	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.2277	1438	3636	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.2106	1259	3636	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	81.4933	1173	3636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:27,984] [INFO] DFAST Taxonomy check result was written to GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:27:27,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:27,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:27,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference/checkm_data
[2024-01-24 11:27:27,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:28,087] [INFO] Task started: CheckM
[2024-01-24 11:27:28,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/checkm_input GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:29:04,745] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:04,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:04,772] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:04,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:04,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:29:04,773] [INFO] Task started: Blastn
[2024-01-24 11:29:04,773] [INFO] Running command: blastn -query GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd401cecf-b20f-475e-a3fb-32f261203ad1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:06,622] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:06,626] [INFO] Selected 6 target genomes.
[2024-01-24 11:29:06,626] [INFO] Target genome list was writen to GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:06,649] [INFO] Task started: fastANI
[2024-01-24 11:29:06,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg7504c0ad-b984-48e3-9918-1ceba5a54643/GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna.gz --refList GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:31,216] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:31,224] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:31,224] [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_002902965.1	s__Paraburkholderia hospita	99.7671	3432	3636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	conclusive
GCF_002902925.1	s__Paraburkholderia terrae	95.215	2704	3636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	-
GCF_013426915.1	s__Paraburkholderia sp013426915	93.9539	2658	3636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013426895.1	s__Paraburkholderia sp013426895	92.7897	2523	3636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902945.1	s__Paraburkholderia caribensis	92.7561	2334	3636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.86	96.01	0.91	0.80	9	-
GCF_017104715.1	s__Paraburkholderia sp017104715	88.4983	2334	3636	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 11:29:31,226] [INFO] GTDB search result was written to GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:31,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:31,229] [INFO] DFAST_QC result json was written to GCF_900108355.1_IMG-taxon_2654588150_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:29:31,229] [INFO] DFAST_QC completed!
[2024-01-24 11:29:31,229] [INFO] Total running time: 0h3m10s