[2024-01-24 11:59:51,986] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,990] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference
[2024-01-24 11:59:55,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,382] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1cdac81-f622-494f-8840-f2119b1ad005/GCF_002917095.1_ASM291709v1_genomic.fna.gz | prodigal -d GCF_002917095.1_ASM291709v1_genomic.fna/cds.fna -a GCF_002917095.1_ASM291709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:17,491] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:17,491] [INFO] Task started: HMMsearch
[2024-01-24 12:00:17,491] [INFO] Running command: hmmsearch --tblout GCF_002917095.1_ASM291709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference/reference_markers.hmm GCF_002917095.1_ASM291709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:17,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:17,818] [INFO] Found 6/6 markers.
[2024-01-24 12:00:17,873] [INFO] Query marker FASTA was written to GCF_002917095.1_ASM291709v1_genomic.fna/markers.fasta
[2024-01-24 12:00:17,874] [INFO] Task started: Blastn
[2024-01-24 12:00:17,874] [INFO] Running command: blastn -query GCF_002917095.1_ASM291709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference/reference_markers.fasta -out GCF_002917095.1_ASM291709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:18,841] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:18,844] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:18,845] [INFO] Target genome list was writen to GCF_002917095.1_ASM291709v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:18,869] [INFO] Task started: fastANI
[2024-01-24 12:00:18,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1cdac81-f622-494f-8840-f2119b1ad005/GCF_002917095.1_ASM291709v1_genomic.fna.gz --refList GCF_002917095.1_ASM291709v1_genomic.fna/target_genomes.txt --output GCF_002917095.1_ASM291709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:44,509] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:44,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:44,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:44,524] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:44,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:44,524] [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 eburnea	strain=JCM 18070	GCA_002917095.1	1189126	1189126	type	True	100.0	2284	2286	95	conclusive
Paraburkholderia bannensis	strain=NBRC 103871	GCA_000685015.1	765414	765414	type	True	90.2165	1814	2286	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_900109265.1	92647	92647	type	True	86.79	1625	2286	95	below_threshold
Paraburkholderia tropica	strain=Ppe8	GCA_002071575.1	92647	92647	type	True	86.7829	1642	2286	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_902833865.1	92647	92647	type	True	86.7625	1639	2286	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	86.06	1578	2286	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	86.0593	1528	2286	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	85.9746	1560	2286	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	85.745	1379	2286	95	below_threshold
Paraburkholderia acidisoli	strain=DHF22	GCA_009789675.1	2571748	2571748	type	True	85.2617	1444	2286	95	below_threshold
Paraburkholderia hiiakae	strain=LMG 27952	GCA_904848665.1	1081782	1081782	type	True	84.7804	1469	2286	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.4614	1082	2286	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.3033	1169	2286	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	81.0978	975	2286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:44,526] [INFO] DFAST Taxonomy check result was written to GCF_002917095.1_ASM291709v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:44,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:44,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:44,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference/checkm_data
[2024-01-24 12:00:44,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:44,593] [INFO] Task started: CheckM
[2024-01-24 12:00:44,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002917095.1_ASM291709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002917095.1_ASM291709v1_genomic.fna/checkm_input GCF_002917095.1_ASM291709v1_genomic.fna/checkm_result
[2024-01-24 12:01:47,096] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:47,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:47,125] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:47,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:47,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002917095.1_ASM291709v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:47,126] [INFO] Task started: Blastn
[2024-01-24 12:01:47,127] [INFO] Running command: blastn -query GCF_002917095.1_ASM291709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e948a7-1288-49c9-ac6d-a7f6b190488e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002917095.1_ASM291709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:49,061] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:49,066] [INFO] Selected 9 target genomes.
[2024-01-24 12:01:49,066] [INFO] Target genome list was writen to GCF_002917095.1_ASM291709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:49,073] [INFO] Task started: fastANI
[2024-01-24 12:01:49,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1cdac81-f622-494f-8840-f2119b1ad005/GCF_002917095.1_ASM291709v1_genomic.fna.gz --refList GCF_002917095.1_ASM291709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002917095.1_ASM291709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:06,378] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:06,392] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:06,392] [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_002917095.1	s__Paraburkholderia eburnea	100.0	2284	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.11	98.22	0.96	0.92	3	conclusive
GCF_000685015.1	s__Paraburkholderia bannensis	90.2044	1816	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753055.1	s__Paraburkholderia sp011753055	89.7288	1806	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200455.1	s__Paraburkholderia bannensis_A	89.4912	1765	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017104965.1	s__Paraburkholderia sp017104965	88.8192	1760	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109265.1	s__Paraburkholderia tropica	86.8204	1621	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.07	95.97	0.93	0.85	14	-
GCF_009789675.1	s__Paraburkholderia acidisoli	85.2728	1442	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268775.1	s__Paraburkholderia unamae	85.2323	1489	2286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.69	98.69	0.91	0.91	2	-
GCF_904848665.1	s__Paraburkholderia hiiakae	84.7742	1471	2286	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 12:02:06,395] [INFO] GTDB search result was written to GCF_002917095.1_ASM291709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:06,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:06,399] [INFO] DFAST_QC result json was written to GCF_002917095.1_ASM291709v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:06,400] [INFO] DFAST_QC completed!
[2024-01-24 12:02:06,400] [INFO] Total running time: 0h2m14s