[2024-01-24 15:18:36,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:36,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:36,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference
[2024-01-24 15:18:38,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,356] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c123d52-9726-4f8b-bbbb-80ae3c55b7df/GCF_902459565.1_LMG_31011_genomic.fna.gz | prodigal -d GCF_902459565.1_LMG_31011_genomic.fna/cds.fna -a GCF_902459565.1_LMG_31011_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:00,616] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:00,616] [INFO] Task started: HMMsearch
[2024-01-24 15:19:00,616] [INFO] Running command: hmmsearch --tblout GCF_902459565.1_LMG_31011_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference/reference_markers.hmm GCF_902459565.1_LMG_31011_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:01,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:01,011] [INFO] Found 6/6 markers.
[2024-01-24 15:19:01,092] [INFO] Query marker FASTA was written to GCF_902459565.1_LMG_31011_genomic.fna/markers.fasta
[2024-01-24 15:19:01,093] [INFO] Task started: Blastn
[2024-01-24 15:19:01,093] [INFO] Running command: blastn -query GCF_902459565.1_LMG_31011_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference/reference_markers.fasta -out GCF_902459565.1_LMG_31011_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:02,078] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:02,081] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:02,082] [INFO] Target genome list was writen to GCF_902459565.1_LMG_31011_genomic.fna/target_genomes.txt
[2024-01-24 15:19:02,089] [INFO] Task started: fastANI
[2024-01-24 15:19:02,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c123d52-9726-4f8b-bbbb-80ae3c55b7df/GCF_902459565.1_LMG_31011_genomic.fna.gz --refList GCF_902459565.1_LMG_31011_genomic.fna/target_genomes.txt --output GCF_902459565.1_LMG_31011_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:20,045] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:20,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:20,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:20,056] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:20,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:20,057] [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
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	100.0	1978	1978	95	conclusive
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	93.2999	1730	1978	95	below_threshold
Pandoraea anapnoica	strain=LMG 31117	GCA_902459765.1	2508301	2508301	type	True	93.0035	1688	1978	95	below_threshold
Pandoraea sputorum	strain=NCTC13161	GCA_900187205.1	93222	93222	type	True	92.7156	1713	1978	95	below_threshold
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	92.6954	1719	1978	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	92.4741	1613	1978	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.6743	588	1978	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.5779	474	1978	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.4719	521	1978	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.2604	493	1978	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.1041	404	1978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,059] [INFO] DFAST Taxonomy check result was written to GCF_902459565.1_LMG_31011_genomic.fna/tc_result.tsv
[2024-01-24 15:19:20,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:20,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:20,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference/checkm_data
[2024-01-24 15:19:20,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:20,119] [INFO] Task started: CheckM
[2024-01-24 15:19:20,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459565.1_LMG_31011_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459565.1_LMG_31011_genomic.fna/checkm_input GCF_902459565.1_LMG_31011_genomic.fna/checkm_result
[2024-01-24 15:20:22,380] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:22,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:22,404] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:22,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:22,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459565.1_LMG_31011_genomic.fna/markers.fasta)
[2024-01-24 15:20:22,405] [INFO] Task started: Blastn
[2024-01-24 15:20:22,405] [INFO] Running command: blastn -query GCF_902459565.1_LMG_31011_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a58c2f1-e0bd-49ee-8543-d3dd4557e96b/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459565.1_LMG_31011_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:24,101] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:24,105] [INFO] Selected 5 target genomes.
[2024-01-24 15:20:24,105] [INFO] Target genome list was writen to GCF_902459565.1_LMG_31011_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:24,110] [INFO] Task started: fastANI
[2024-01-24 15:20:24,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c123d52-9726-4f8b-bbbb-80ae3c55b7df/GCF_902459565.1_LMG_31011_genomic.fna.gz --refList GCF_902459565.1_LMG_31011_genomic.fna/target_genomes_gtdb.txt --output GCF_902459565.1_LMG_31011_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:32,653] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:32,659] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:32,660] [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_902459565.1	s__Pandoraea aquatica	100.0	1978	1978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902459615.1	s__Pandoraea commovens	93.2999	1730	1978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459765.1	s__Pandoraea anapnoica	92.9988	1689	1978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814845.2	s__Pandoraea sputorum	92.6954	1719	1978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
GCF_000972785.3	s__Pandoraea oxalativorans	92.4741	1613	1978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:32,663] [INFO] GTDB search result was written to GCF_902459565.1_LMG_31011_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:32,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:32,667] [INFO] DFAST_QC result json was written to GCF_902459565.1_LMG_31011_genomic.fna/dqc_result.json
[2024-01-24 15:20:32,667] [INFO] DFAST_QC completed!
[2024-01-24 15:20:32,667] [INFO] Total running time: 0h1m57s