[2024-01-24 13:36:43,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:43,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:43,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference
[2024-01-24 13:36:45,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,060] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,060] [INFO] Running command: gunzip -c /var/lib/cwl/stga9ce549e-3c33-4a58-a1d4-18eef1202ba1/GCF_009455635.1_ASM945563v1_genomic.fna.gz | prodigal -d GCF_009455635.1_ASM945563v1_genomic.fna/cds.fna -a GCF_009455635.1_ASM945563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:17,201] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:17,201] [INFO] Task started: HMMsearch
[2024-01-24 13:37:17,202] [INFO] Running command: hmmsearch --tblout GCF_009455635.1_ASM945563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference/reference_markers.hmm GCF_009455635.1_ASM945563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:17,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:17,583] [INFO] Found 6/6 markers.
[2024-01-24 13:37:17,649] [INFO] Query marker FASTA was written to GCF_009455635.1_ASM945563v1_genomic.fna/markers.fasta
[2024-01-24 13:37:17,650] [INFO] Task started: Blastn
[2024-01-24 13:37:17,650] [INFO] Running command: blastn -query GCF_009455635.1_ASM945563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference/reference_markers.fasta -out GCF_009455635.1_ASM945563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:18,599] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:18,602] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:18,603] [INFO] Target genome list was writen to GCF_009455635.1_ASM945563v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:18,621] [INFO] Task started: fastANI
[2024-01-24 13:37:18,621] [INFO] Running command: fastANI --query /var/lib/cwl/stga9ce549e-3c33-4a58-a1d4-18eef1202ba1/GCF_009455635.1_ASM945563v1_genomic.fna.gz --refList GCF_009455635.1_ASM945563v1_genomic.fna/target_genomes.txt --output GCF_009455635.1_ASM945563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:45,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:45,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:45,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:45,445] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:37:45,445] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:45,445] [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 agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	100.0	2903	2906	95	inconclusive
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	95.6856	2180	2906	95	inconclusive
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	95.5868	2177	2906	95	inconclusive
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	95.572	2060	2906	95	inconclusive
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	90.2546	1796	2906	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	89.5669	1876	2906	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	89.4845	1867	2906	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	89.479	1950	2906	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	89.2914	1903	2906	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	89.217	1988	2906	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.0807	1167	2906	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.7883	1341	2906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:45,447] [INFO] DFAST Taxonomy check result was written to GCF_009455635.1_ASM945563v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:45,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:45,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:45,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference/checkm_data
[2024-01-24 13:37:45,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:45,528] [INFO] Task started: CheckM
[2024-01-24 13:37:45,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009455635.1_ASM945563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009455635.1_ASM945563v1_genomic.fna/checkm_input GCF_009455635.1_ASM945563v1_genomic.fna/checkm_result
[2024-01-24 13:39:10,014] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:10,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:10,045] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:10,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:10,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009455635.1_ASM945563v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:10,046] [INFO] Task started: Blastn
[2024-01-24 13:39:10,046] [INFO] Running command: blastn -query GCF_009455635.1_ASM945563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fbaf797-d812-4317-8bf4-0c700c77d118/dqc_reference/reference_markers_gtdb.fasta -out GCF_009455635.1_ASM945563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:11,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:11,790] [INFO] Selected 16 target genomes.
[2024-01-24 13:39:11,791] [INFO] Target genome list was writen to GCF_009455635.1_ASM945563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:11,837] [INFO] Task started: fastANI
[2024-01-24 13:39:11,837] [INFO] Running command: fastANI --query /var/lib/cwl/stga9ce549e-3c33-4a58-a1d4-18eef1202ba1/GCF_009455635.1_ASM945563v1_genomic.fna.gz --refList GCF_009455635.1_ASM945563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009455635.1_ASM945563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:47,215] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:47,228] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:47,229] [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_902833645.1	s__Paraburkholderia fungorum	95.5965	2176	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.62	95.59	0.90	0.75	14	conclusive
GCF_003610895.1	s__Paraburkholderia fungorum_B	90.9071	2249	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	90.2681	1794	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	90.0474	1549	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	89.8576	1967	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610295.1	s__Paraburkholderia sp003610295	89.6487	1904	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	89.5961	1857	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_905220975.1	s__Paraburkholderia sp905220975	89.5927	1872	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	89.5916	2121	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_900230185.1	s__Paraburkholderia sp900230185	89.506	1986	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177695.1	s__Paraburkholderia sp013177695	89.4762	1867	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116445.1	s__Paraburkholderia aspalathi	89.395	1950	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_905220835.1	s__Paraburkholderia sp905220835	89.2981	1893	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_902859805.1	s__Paraburkholderia sediminicola	89.2261	1987	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	89.1459	1837	2906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003353175.1	s__Paraburkholderia lacunae	86.3927	1560	2906	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 13:39:47,230] [INFO] GTDB search result was written to GCF_009455635.1_ASM945563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:47,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:47,234] [INFO] DFAST_QC result json was written to GCF_009455635.1_ASM945563v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:47,234] [INFO] DFAST_QC completed!
[2024-01-24 13:39:47,235] [INFO] Total running time: 0h3m3s