[2024-01-24 12:28:34,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,496] [INFO] DQC Reference Directory: /var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference
[2024-01-24 12:28:35,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,711] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgb58c9389-f422-4b47-87e1-df9ca4646158/GCF_014636375.1_ASM1463637v1_genomic.fna.gz | prodigal -d GCF_014636375.1_ASM1463637v1_genomic.fna/cds.fna -a GCF_014636375.1_ASM1463637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:56,063] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:56,063] [INFO] Task started: HMMsearch
[2024-01-24 12:28:56,063] [INFO] Running command: hmmsearch --tblout GCF_014636375.1_ASM1463637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference/reference_markers.hmm GCF_014636375.1_ASM1463637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:56,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:56,406] [INFO] Found 6/6 markers.
[2024-01-24 12:28:56,463] [INFO] Query marker FASTA was written to GCF_014636375.1_ASM1463637v1_genomic.fna/markers.fasta
[2024-01-24 12:28:56,463] [INFO] Task started: Blastn
[2024-01-24 12:28:56,463] [INFO] Running command: blastn -query GCF_014636375.1_ASM1463637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference/reference_markers.fasta -out GCF_014636375.1_ASM1463637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:57,457] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:57,462] [INFO] Selected 16 target genomes.
[2024-01-24 12:28:57,462] [INFO] Target genome list was writen to GCF_014636375.1_ASM1463637v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:57,519] [INFO] Task started: fastANI
[2024-01-24 12:28:57,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb58c9389-f422-4b47-87e1-df9ca4646158/GCF_014636375.1_ASM1463637v1_genomic.fna.gz --refList GCF_014636375.1_ASM1463637v1_genomic.fna/target_genomes.txt --output GCF_014636375.1_ASM1463637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:24,365] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:24,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:24,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:24,381] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:29:24,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:24,381] [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
Caballeronia grimmiae	strain=CGMCC 1.11013	GCA_014636375.1	1071679	1071679	type	True	100.0	2210	2211	95	conclusive
Caballeronia grimmiae	strain=R27	GCA_000698555.1	1071679	1071679	type	True	99.9701	2142	2211	95	conclusive
Caballeronia concitans		GCA_001544615.2	1777133	1777133	type	True	88.6699	1556	2211	95	below_threshold
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	85.4515	1472	2211	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	85.2578	1525	2211	95	below_threshold
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	85.2279	1360	2211	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	85.2258	1540	2211	95	below_threshold
Caballeronia ptereochthonis		GCA_001545075.2	1777144	1777144	type	True	85.1185	1434	2211	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	85.0494	1485	2211	95	below_threshold
Caballeronia arvi		GCA_001544695.2	1777135	1777135	type	True	84.9742	1499	2211	95	below_threshold
Caballeronia hypogeia		GCA_001544875.2	1777140	1777140	type	True	84.8258	1457	2211	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.0032	1105	2211	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	80.9408	1005	2211	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	80.6619	904	2211	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	80.4734	913	2211	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.3455	951	2211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:24,384] [INFO] DFAST Taxonomy check result was written to GCF_014636375.1_ASM1463637v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:24,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:24,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:24,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference/checkm_data
[2024-01-24 12:29:24,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:24,451] [INFO] Task started: CheckM
[2024-01-24 12:29:24,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636375.1_ASM1463637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636375.1_ASM1463637v1_genomic.fna/checkm_input GCF_014636375.1_ASM1463637v1_genomic.fna/checkm_result
[2024-01-24 12:30:23,397] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:23,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:23,434] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:23,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:23,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636375.1_ASM1463637v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:23,436] [INFO] Task started: Blastn
[2024-01-24 12:30:23,436] [INFO] Running command: blastn -query GCF_014636375.1_ASM1463637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0176bae-9898-4034-9476-019a4834e927/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636375.1_ASM1463637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:25,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:25,319] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:25,319] [INFO] Target genome list was writen to GCF_014636375.1_ASM1463637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:25,348] [INFO] Task started: fastANI
[2024-01-24 12:30:25,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgb58c9389-f422-4b47-87e1-df9ca4646158/GCF_014636375.1_ASM1463637v1_genomic.fna.gz --refList GCF_014636375.1_ASM1463637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636375.1_ASM1463637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:46,750] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:46,766] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:46,766] [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_000698555.1	s__Caballeronia grimmiae	99.9701	2142	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001544615.1	s__Caballeronia concitans	88.6622	1556	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.76	99.76	0.97	0.97	2	-
GCF_017220215.1	s__Caballeronia sp902833455	86.124	1455	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.21	98.21	0.98	0.98	2	-
GCF_902506145.1	s__Caballeronia sp902506145	86.0193	1452	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900044055.2	s__Caballeronia calidae	85.432	1474	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258035.1	s__Caballeronia novacaledonica	85.2656	1355	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544575.2	s__Caballeronia cordobensis	85.2413	1526	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	-
GCA_001580565.1	s__Caballeronia megalochromosomata	85.1246	1444	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545075.1	s__Caballeronia ptereochthonis	85.1084	1435	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544915.2	s__Caballeronia pedi	85.069	1483	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544695.2	s__Caballeronia arvi	84.9844	1497	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001189335.2	s__Caballeronia schumannianae_A	84.9118	502	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.68	95.68	0.80	0.80	2	-
GCF_001544875.2	s__Caballeronia hypogeia	84.8383	1455	2211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:46,768] [INFO] GTDB search result was written to GCF_014636375.1_ASM1463637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:46,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:46,773] [INFO] DFAST_QC result json was written to GCF_014636375.1_ASM1463637v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:46,774] [INFO] DFAST_QC completed!
[2024-01-24 12:30:46,774] [INFO] Total running time: 0h2m12s