[2024-01-25 17:52:20,715] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:20,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:20,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference
[2024-01-25 17:52:21,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:21,913] [INFO] Task started: Prodigal
[2024-01-25 17:52:21,914] [INFO] Running command: gunzip -c /var/lib/cwl/stgb75fc9e0-60b2-4164-b990-fb70a83ff36a/GCF_001545075.1_ASM154507v2_genomic.fna.gz | prodigal -d GCF_001545075.1_ASM154507v2_genomic.fna/cds.fna -a GCF_001545075.1_ASM154507v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:42,538] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:42,539] [INFO] Task started: HMMsearch
[2024-01-25 17:52:42,539] [INFO] Running command: hmmsearch --tblout GCF_001545075.1_ASM154507v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference/reference_markers.hmm GCF_001545075.1_ASM154507v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:42,870] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:42,872] [INFO] Found 6/6 markers.
[2024-01-25 17:52:42,928] [INFO] Query marker FASTA was written to GCF_001545075.1_ASM154507v2_genomic.fna/markers.fasta
[2024-01-25 17:52:42,928] [INFO] Task started: Blastn
[2024-01-25 17:52:42,928] [INFO] Running command: blastn -query GCF_001545075.1_ASM154507v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference/reference_markers.fasta -out GCF_001545075.1_ASM154507v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:43,935] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:43,938] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:43,938] [INFO] Target genome list was writen to GCF_001545075.1_ASM154507v2_genomic.fna/target_genomes.txt
[2024-01-25 17:52:43,943] [INFO] Task started: fastANI
[2024-01-25 17:52:43,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgb75fc9e0-60b2-4164-b990-fb70a83ff36a/GCF_001545075.1_ASM154507v2_genomic.fna.gz --refList GCF_001545075.1_ASM154507v2_genomic.fna/target_genomes.txt --output GCF_001545075.1_ASM154507v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:12,268] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:12,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:12,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:12,278] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:12,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:12,278] [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 ptereochthonis		GCA_001545075.2	1777144	1777144	type	True	100.0	2518	2522	95	conclusive
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	88.7048	1758	2522	95	below_threshold
Caballeronia insecticola	strain=RPE64	GCA_000402035.1	758793	758793	type	True	88.5752	1746	2522	95	below_threshold
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	88.3834	1626	2522	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	88.3013	1772	2522	95	below_threshold
Caballeronia temeraria		GCA_001544795.2	1777137	1777137	type	True	87.9225	1755	2522	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	87.9141	1715	2522	95	below_threshold
Caballeronia glebae		GCA_001545035.2	1777143	1777143	type	True	87.8349	1720	2522	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	87.7716	1763	2522	95	below_threshold
Caballeronia hypogeia		GCA_001544875.2	1777140	1777140	type	True	87.6682	1716	2522	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.4021	1266	2522	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.2736	1145	2522	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.9296	1168	2522	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	80.8904	989	2522	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	80.7321	1021	2522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:12,280] [INFO] DFAST Taxonomy check result was written to GCF_001545075.1_ASM154507v2_genomic.fna/tc_result.tsv
[2024-01-25 17:53:12,280] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:12,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:12,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference/checkm_data
[2024-01-25 17:53:12,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:12,354] [INFO] Task started: CheckM
[2024-01-25 17:53:12,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001545075.1_ASM154507v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001545075.1_ASM154507v2_genomic.fna/checkm_input GCF_001545075.1_ASM154507v2_genomic.fna/checkm_result
[2024-01-25 17:54:23,125] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:23,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:23,146] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:23,146] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:23,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001545075.1_ASM154507v2_genomic.fna/markers.fasta)
[2024-01-25 17:54:23,148] [INFO] Task started: Blastn
[2024-01-25 17:54:23,148] [INFO] Running command: blastn -query GCF_001545075.1_ASM154507v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6936d0d2-4959-4b57-ad37-dab47b93079c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001545075.1_ASM154507v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:25,247] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:25,250] [INFO] Selected 12 target genomes.
[2024-01-25 17:54:25,250] [INFO] Target genome list was writen to GCF_001545075.1_ASM154507v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:25,263] [INFO] Task started: fastANI
[2024-01-25 17:54:25,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgb75fc9e0-60b2-4164-b990-fb70a83ff36a/GCF_001545075.1_ASM154507v2_genomic.fna.gz --refList GCF_001545075.1_ASM154507v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001545075.1_ASM154507v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:48,910] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:48,918] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:48,918] [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_001545075.1	s__Caballeronia ptereochthonis	100.0	2518	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001189345.1	s__Caballeronia kirkii_B	92.7617	1099	2522	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	89.6571	564	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.68	95.68	0.80	0.80	2	-
GCA_001544595.2	s__Caballeronia peredens	89.5191	1639	2522	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	88.6768	1762	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000402035.1	s__Caballeronia insecticola	88.6105	1741	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001580565.1	s__Caballeronia megalochromosomata	88.4418	1770	2522	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	88.387	1625	2522	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	88.3281	1767	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018408855.1	s__Caballeronia sp018408855	88.1891	1806	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.23	98.23	0.88	0.88	2	-
GCA_001544655.2	s__Caballeronia turbans	88.1078	1697	2522	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	87.9076	1716	2522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:48,920] [INFO] GTDB search result was written to GCF_001545075.1_ASM154507v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:48,920] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:48,923] [INFO] DFAST_QC result json was written to GCF_001545075.1_ASM154507v2_genomic.fna/dqc_result.json
[2024-01-25 17:54:48,923] [INFO] DFAST_QC completed!
[2024-01-25 17:54:48,923] [INFO] Total running time: 0h2m28s