[2024-01-25 18:15:35,658] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference
[2024-01-25 18:15:36,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,795] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg52398d8e-b6d5-461b-aa50-b699192c45a9/GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna.gz | prodigal -d GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/cds.fna -a GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:03,877] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:03,877] [INFO] Task started: HMMsearch
[2024-01-25 18:16:03,877] [INFO] Running command: hmmsearch --tblout GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference/reference_markers.hmm GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:04,309] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:04,310] [INFO] Found 6/6 markers.
[2024-01-25 18:16:04,384] [INFO] Query marker FASTA was written to GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/markers.fasta
[2024-01-25 18:16:04,384] [INFO] Task started: Blastn
[2024-01-25 18:16:04,384] [INFO] Running command: blastn -query GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/markers.fasta -db /var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference/reference_markers.fasta -out GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:05,316] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:05,318] [INFO] Selected 13 target genomes.
[2024-01-25 18:16:05,319] [INFO] Target genome list was writen to GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/target_genomes.txt
[2024-01-25 18:16:05,326] [INFO] Task started: fastANI
[2024-01-25 18:16:05,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg52398d8e-b6d5-461b-aa50-b699192c45a9/GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna.gz --refList GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/target_genomes.txt --output GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:31,974] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:31,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:31,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:31,985] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:16:31,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:16:31,986] [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_000013645.1	36873	36873	type	True	94.6934	2225	2781	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	94.6776	2218	2781	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	91.1839	2032	2781	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	89.567	1869	2781	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	89.5508	1841	2781	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.7878	1507	2781	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	86.7425	1691	2781	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	86.6703	1602	2781	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.6514	1695	2781	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.466	1579	2781	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.43	1657	2781	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.7416	1246	2781	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.4873	1427	2781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:31,987] [INFO] DFAST Taxonomy check result was written to GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/tc_result.tsv
[2024-01-25 18:16:31,988] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:31,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:31,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference/checkm_data
[2024-01-25 18:16:31,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:32,066] [INFO] Task started: CheckM
[2024-01-25 18:16:32,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/checkm_input GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/checkm_result
[2024-01-25 18:17:46,489] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:46,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:46,509] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:46,510] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:46,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/markers.fasta)
[2024-01-25 18:17:46,511] [INFO] Task started: Blastn
[2024-01-25 18:17:46,511] [INFO] Running command: blastn -query GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/markers.fasta -db /var/lib/cwl/stg5727ea30-ed2c-4e5e-8ce3-fee6f0c5788f/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:48,309] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:48,314] [INFO] Selected 9 target genomes.
[2024-01-25 18:17:48,314] [INFO] Target genome list was writen to GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:48,328] [INFO] Task started: fastANI
[2024-01-25 18:17:48,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg52398d8e-b6d5-461b-aa50-b699192c45a9/GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna.gz --refList GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/target_genomes_gtdb.txt --output GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:08,131] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:08,138] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:08,138] [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_902459535.1	s__Paraburkholderia sp000178415	100.0	2775	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	conclusive
GCF_000013645.1	s__Paraburkholderia xenovorans	94.7015	2223	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	91.1799	2033	2781	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	91.0087	2022	2781	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	90.2378	1868	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	89.9216	1925	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020125.1	s__Paraburkholderia phytofirmans	89.5448	1840	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_003002025.1	s__Paraburkholderia sp003002025	89.4288	1802	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_902859915.1	s__Paraburkholderia ultramafica	87.7955	1506	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:18:08,139] [INFO] GTDB search result was written to GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:08,140] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:08,142] [INFO] DFAST_QC result json was written to GCF_902459535.1_Paraburkholderia_sp_Msb3_genomic.fna/dqc_result.json
[2024-01-25 18:18:08,142] [INFO] DFAST_QC completed!
[2024-01-25 18:18:08,142] [INFO] Total running time: 0h2m32s