[2024-01-24 13:17:44,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:44,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:44,385] [INFO] DQC Reference Directory: /var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference
[2024-01-24 13:17:45,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:45,619] [INFO] Task started: Prodigal
[2024-01-24 13:17:45,619] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2270443-d9d0-42f7-9b75-95c9b1f54deb/GCF_000020125.1_ASM2012v1_genomic.fna.gz | prodigal -d GCF_000020125.1_ASM2012v1_genomic.fna/cds.fna -a GCF_000020125.1_ASM2012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:13,349] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:13,349] [INFO] Task started: HMMsearch
[2024-01-24 13:18:13,350] [INFO] Running command: hmmsearch --tblout GCF_000020125.1_ASM2012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference/reference_markers.hmm GCF_000020125.1_ASM2012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:13,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:13,825] [INFO] Found 6/6 markers.
[2024-01-24 13:18:13,888] [INFO] Query marker FASTA was written to GCF_000020125.1_ASM2012v1_genomic.fna/markers.fasta
[2024-01-24 13:18:13,888] [INFO] Task started: Blastn
[2024-01-24 13:18:13,888] [INFO] Running command: blastn -query GCF_000020125.1_ASM2012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference/reference_markers.fasta -out GCF_000020125.1_ASM2012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:14,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:14,962] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:14,962] [INFO] Target genome list was writen to GCF_000020125.1_ASM2012v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:14,968] [INFO] Task started: fastANI
[2024-01-24 13:18:14,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2270443-d9d0-42f7-9b75-95c9b1f54deb/GCF_000020125.1_ASM2012v1_genomic.fna.gz --refList GCF_000020125.1_ASM2012v1_genomic.fna/target_genomes.txt --output GCF_000020125.1_ASM2012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:44,516] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:44,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:44,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:44,529] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:44,529] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:44,530] [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 phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	100.0	2734	2737	95	inconclusive
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	95.792	2254	2737	95	inconclusive
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	89.3742	1937	2737	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	89.1966	1882	2737	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	89.1927	1867	2737	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.8552	1539	2737	95	below_threshold
Paraburkholderia ginsengiterrae	strain=DCY85	GCA_001645125.1	1462993	1462993	type	True	87.526	1685	2737	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.6774	1665	2737	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.6575	1838	2737	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	86.6323	1662	2737	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.511	1756	2737	95	below_threshold
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	86.2608	1789	2737	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.8856	1284	2737	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.6087	1450	2737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,531] [INFO] DFAST Taxonomy check result was written to GCF_000020125.1_ASM2012v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:44,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:44,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:44,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference/checkm_data
[2024-01-24 13:18:44,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:44,620] [INFO] Task started: CheckM
[2024-01-24 13:18:44,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020125.1_ASM2012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020125.1_ASM2012v1_genomic.fna/checkm_input GCF_000020125.1_ASM2012v1_genomic.fna/checkm_result
[2024-01-24 13:20:02,236] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:02,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:02,262] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:02,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:02,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020125.1_ASM2012v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:02,264] [INFO] Task started: Blastn
[2024-01-24 13:20:02,264] [INFO] Running command: blastn -query GCF_000020125.1_ASM2012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9834c9a-0f05-4154-adee-525c583b5aee/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020125.1_ASM2012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:04,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:04,376] [INFO] Selected 7 target genomes.
[2024-01-24 13:20:04,376] [INFO] Target genome list was writen to GCF_000020125.1_ASM2012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:04,386] [INFO] Task started: fastANI
[2024-01-24 13:20:04,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2270443-d9d0-42f7-9b75-95c9b1f54deb/GCF_000020125.1_ASM2012v1_genomic.fna.gz --refList GCF_000020125.1_ASM2012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020125.1_ASM2012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:20,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:20,252] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:20,252] [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_000020125.1	s__Paraburkholderia phytofirmans	100.0	2734	2737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	conclusive
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	93.1151	2146	2737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002025.1	s__Paraburkholderia sp003002025	93.0371	2076	2737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_004339745.1	s__Paraburkholderia sp004339745	91.9371	2068	2737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459535.1	s__Paraburkholderia sp000178415	89.5247	1857	2737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_900104795.1	s__Paraburkholderia sp900104795	89.3674	1945	2737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.49	98.44	0.88	0.86	5	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	89.3648	1939	2737	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 13:20:20,254] [INFO] GTDB search result was written to GCF_000020125.1_ASM2012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:20,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:20,258] [INFO] DFAST_QC result json was written to GCF_000020125.1_ASM2012v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:20,258] [INFO] DFAST_QC completed!
[2024-01-24 13:20:20,258] [INFO] Total running time: 0h2m36s