[2024-01-24 12:47:27,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:27,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:27,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference
[2024-01-24 12:47:28,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:28,554] [INFO] Task started: Prodigal
[2024-01-24 12:47:28,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg66243a8c-a35a-44b3-a9d4-7861a9233177/GCF_000020045.1_ASM2004v1_genomic.fna.gz | prodigal -d GCF_000020045.1_ASM2004v1_genomic.fna/cds.fna -a GCF_000020045.1_ASM2004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:59,110] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:59,110] [INFO] Task started: HMMsearch
[2024-01-24 12:47:59,110] [INFO] Running command: hmmsearch --tblout GCF_000020045.1_ASM2004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference/reference_markers.hmm GCF_000020045.1_ASM2004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:59,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:59,520] [INFO] Found 6/6 markers.
[2024-01-24 12:47:59,589] [INFO] Query marker FASTA was written to GCF_000020045.1_ASM2004v1_genomic.fna/markers.fasta
[2024-01-24 12:47:59,589] [INFO] Task started: Blastn
[2024-01-24 12:47:59,589] [INFO] Running command: blastn -query GCF_000020045.1_ASM2004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference/reference_markers.fasta -out GCF_000020045.1_ASM2004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:00,599] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:00,604] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:00,605] [INFO] Target genome list was writen to GCF_000020045.1_ASM2004v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:00,609] [INFO] Task started: fastANI
[2024-01-24 12:48:00,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg66243a8c-a35a-44b3-a9d4-7861a9233177/GCF_000020045.1_ASM2004v1_genomic.fna.gz --refList GCF_000020045.1_ASM2004v1_genomic.fna/target_genomes.txt --output GCF_000020045.1_ASM2004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:24,244] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:24,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:24,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:24,258] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:48:24,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:24,258] [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 phymatum	strain=STM815	GCA_000020045.1	148447	148447	type	True	100.0	2885	2890	95	conclusive
Paraburkholderia phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	99.9827	2832	2890	95	conclusive
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	89.187	2100	2890	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	89.0594	2121	2890	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	87.1048	1894	2890	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	87.0805	2000	2890	95	below_threshold
Paraburkholderia diazotrophica	strain=LMG 26031	GCA_900108945.1	667676	667676	type	True	86.549	1838	2890	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.0219	1136	2890	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.9516	1312	2890	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	81.7508	1166	2890	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	81.3885	1166	2890	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:24,261] [INFO] DFAST Taxonomy check result was written to GCF_000020045.1_ASM2004v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:24,262] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:24,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:24,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference/checkm_data
[2024-01-24 12:48:24,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:24,351] [INFO] Task started: CheckM
[2024-01-24 12:48:24,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020045.1_ASM2004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020045.1_ASM2004v1_genomic.fna/checkm_input GCF_000020045.1_ASM2004v1_genomic.fna/checkm_result
[2024-01-24 12:49:47,959] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:47,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:47,987] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:47,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:47,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020045.1_ASM2004v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:47,988] [INFO] Task started: Blastn
[2024-01-24 12:49:47,988] [INFO] Running command: blastn -query GCF_000020045.1_ASM2004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8955f3-48f1-4d08-9a40-e95b8e716c22/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020045.1_ASM2004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:49,858] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:49,863] [INFO] Selected 9 target genomes.
[2024-01-24 12:49:49,863] [INFO] Target genome list was writen to GCF_000020045.1_ASM2004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:49,882] [INFO] Task started: fastANI
[2024-01-24 12:49:49,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg66243a8c-a35a-44b3-a9d4-7861a9233177/GCF_000020045.1_ASM2004v1_genomic.fna.gz --refList GCF_000020045.1_ASM2004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020045.1_ASM2004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:10,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:10,993] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:10,993] [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_000020045.1	s__Paraburkholderia phymatum	100.0	2885	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017104565.1	s__Paraburkholderia sp017104565	91.4192	2029	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848645.1	s__Paraburkholderia sabiae	89.1898	2100	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995085.1	s__Paraburkholderia azotifigens	89.0747	2118	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.91	98.91	0.86	0.86	2	-
GCF_002902965.1	s__Paraburkholderia hospita	87.1461	2010	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_002902925.1	s__Paraburkholderia terrae	87.0783	1988	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	-
GCF_017104715.1	s__Paraburkholderia sp017104715	86.854	1876	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108945.1	s__Paraburkholderia diazotrophica	86.5293	1842	2890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121405.1	s__Paraburkholderia sp003121405	86.3025	1739	2890	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 12:50:10,994] [INFO] GTDB search result was written to GCF_000020045.1_ASM2004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:10,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:10,998] [INFO] DFAST_QC result json was written to GCF_000020045.1_ASM2004v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:10,998] [INFO] DFAST_QC completed!
[2024-01-24 12:50:10,998] [INFO] Total running time: 0h2m44s