[2024-01-24 13:22:31,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference
[2024-01-24 13:22:32,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,556] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cb7e984-59ee-456d-a7d5-5b0c89c2a8af/GCF_000756045.1_ASM75604v1_genomic.fna.gz | prodigal -d GCF_000756045.1_ASM75604v1_genomic.fna/cds.fna -a GCF_000756045.1_ASM75604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:03,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:03,841] [INFO] Task started: HMMsearch
[2024-01-24 13:23:03,841] [INFO] Running command: hmmsearch --tblout GCF_000756045.1_ASM75604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference/reference_markers.hmm GCF_000756045.1_ASM75604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:04,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:04,243] [INFO] Found 6/6 markers.
[2024-01-24 13:23:04,317] [INFO] Query marker FASTA was written to GCF_000756045.1_ASM75604v1_genomic.fna/markers.fasta
[2024-01-24 13:23:04,318] [INFO] Task started: Blastn
[2024-01-24 13:23:04,318] [INFO] Running command: blastn -query GCF_000756045.1_ASM75604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference/reference_markers.fasta -out GCF_000756045.1_ASM75604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:05,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:05,256] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:05,257] [INFO] Target genome list was writen to GCF_000756045.1_ASM75604v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:06,874] [INFO] Task started: fastANI
[2024-01-24 13:23:06,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb7e984-59ee-456d-a7d5-5b0c89c2a8af/GCF_000756045.1_ASM75604v1_genomic.fna.gz --refList GCF_000756045.1_ASM75604v1_genomic.fna/target_genomes.txt --output GCF_000756045.1_ASM75604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:35,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:35,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:35,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:35,582] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:35,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:35,583] [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 xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	100.0	3231	3233	95	conclusive
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	99.9965	3226	3233	95	conclusive
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	91.0275	2030	3233	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	89.3005	1860	3233	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	89.2187	1888	3233	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.6812	1536	3233	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	87.2271	1571	3233	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	86.8683	1638	3233	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	86.8608	1657	3233	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.6545	1559	3233	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.6028	1703	3233	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.3118	1676	3233	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.7391	1263	3233	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.5823	1455	3233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:35,585] [INFO] DFAST Taxonomy check result was written to GCF_000756045.1_ASM75604v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:35,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:35,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:35,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference/checkm_data
[2024-01-24 13:23:35,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:35,672] [INFO] Task started: CheckM
[2024-01-24 13:23:35,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000756045.1_ASM75604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000756045.1_ASM75604v1_genomic.fna/checkm_input GCF_000756045.1_ASM75604v1_genomic.fna/checkm_result
[2024-01-24 13:25:02,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:02,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:02,364] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:02,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:02,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000756045.1_ASM75604v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:02,366] [INFO] Task started: Blastn
[2024-01-24 13:25:02,366] [INFO] Running command: blastn -query GCF_000756045.1_ASM75604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ca23ee0-c31f-4e77-8a93-1733498c51e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000756045.1_ASM75604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:04,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:04,100] [INFO] Selected 8 target genomes.
[2024-01-24 13:25:04,101] [INFO] Target genome list was writen to GCF_000756045.1_ASM75604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:04,108] [INFO] Task started: fastANI
[2024-01-24 13:25:04,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb7e984-59ee-456d-a7d5-5b0c89c2a8af/GCF_000756045.1_ASM75604v1_genomic.fna.gz --refList GCF_000756045.1_ASM75604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000756045.1_ASM75604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:21,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:21,612] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:21,613] [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_000013645.1	s__Paraburkholderia xenovorans	99.9965	3227	3233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	conclusive
GCF_902459535.1	s__Paraburkholderia sp000178415	94.709	2230	3233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	91.0175	2030	3233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104795.1	s__Paraburkholderia sp900104795	90.7714	2017	3233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.49	98.44	0.88	0.86	5	-
GCF_004339745.1	s__Paraburkholderia sp004339745	89.844	1920	3233	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	89.345	1812	3233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_000020125.1	s__Paraburkholderia phytofirmans	89.2191	1887	3233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_902859915.1	s__Paraburkholderia ultramafica	87.7069	1533	3233	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 13:25:21,614] [INFO] GTDB search result was written to GCF_000756045.1_ASM75604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:21,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:21,620] [INFO] DFAST_QC result json was written to GCF_000756045.1_ASM75604v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:21,620] [INFO] DFAST_QC completed!
[2024-01-24 13:25:21,620] [INFO] Total running time: 0h2m50s