[2024-01-24 14:55:08,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference
[2024-01-24 14:55:10,208] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,209] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,209] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5b22741-71f3-4808-a3eb-793ae5525b63/GCF_008802145.1_ASM880214v1_genomic.fna.gz | prodigal -d GCF_008802145.1_ASM880214v1_genomic.fna/cds.fna -a GCF_008802145.1_ASM880214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:29,568] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:29,568] [INFO] Task started: HMMsearch
[2024-01-24 14:55:29,568] [INFO] Running command: hmmsearch --tblout GCF_008802145.1_ASM880214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference/reference_markers.hmm GCF_008802145.1_ASM880214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:29,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:29,917] [INFO] Found 6/6 markers.
[2024-01-24 14:55:29,978] [INFO] Query marker FASTA was written to GCF_008802145.1_ASM880214v1_genomic.fna/markers.fasta
[2024-01-24 14:55:29,978] [INFO] Task started: Blastn
[2024-01-24 14:55:29,979] [INFO] Running command: blastn -query GCF_008802145.1_ASM880214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference/reference_markers.fasta -out GCF_008802145.1_ASM880214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:31,000] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:31,004] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:31,004] [INFO] Target genome list was writen to GCF_008802145.1_ASM880214v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:31,009] [INFO] Task started: fastANI
[2024-01-24 14:55:31,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5b22741-71f3-4808-a3eb-793ae5525b63/GCF_008802145.1_ASM880214v1_genomic.fna.gz --refList GCF_008802145.1_ASM880214v1_genomic.fna/target_genomes.txt --output GCF_008802145.1_ASM880214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:56,436] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:56,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:56,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:56,458] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:55:56,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:56,458] [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
Burkholderia diffusa	strain=CCUG 54558	GCA_008802145.1	488732	488732	suspected-type	True	100.0	2113	2128	95	conclusive
Burkholderia diffusa		GCA_902499115.1	488732	488732	suspected-type	True	99.9951	2104	2128	95	conclusive
Burkholderia diffusa	strain=DSM 23434	GCA_016836765.1	488732	488732	suspected-type	True	99.9936	2111	2128	95	conclusive
Burkholderia territorii		GCA_902499035.1	1503055	1503055	type	True	93.8322	1675	2128	95	below_threshold
Burkholderia territorii	strain=LMG 28158	GCA_902833055.1	1503055	1503055	type	True	93.7931	1695	2128	95	below_threshold
Burkholderia territorii	strain=CCUG 65687	GCA_008802115.1	1503055	1503055	type	True	93.3513	1245	2128	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	91.9489	1630	2128	95	below_threshold
Burkholderia cepacia	strain=NBRC 14074	GCA_001528845.1	292	292	type	True	90.8199	1705	2128	95	below_threshold
Burkholderia cepacia	strain=ATCC 25416	GCA_000473485.1	292	292	type	True	90.8011	1733	2128	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	88.4314	1486	2128	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	88.3852	1538	2128	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.5463	1209	2128	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.5682	1026	2128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:56,460] [INFO] DFAST Taxonomy check result was written to GCF_008802145.1_ASM880214v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:56,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:56,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:56,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference/checkm_data
[2024-01-24 14:55:56,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:56,535] [INFO] Task started: CheckM
[2024-01-24 14:55:56,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802145.1_ASM880214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802145.1_ASM880214v1_genomic.fna/checkm_input GCF_008802145.1_ASM880214v1_genomic.fna/checkm_result
[2024-01-24 14:56:56,655] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:56,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:56,678] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:56,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:56,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802145.1_ASM880214v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:56,680] [INFO] Task started: Blastn
[2024-01-24 14:56:56,680] [INFO] Running command: blastn -query GCF_008802145.1_ASM880214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a0a2480-7feb-44bc-8bb3-9538a38efe33/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802145.1_ASM880214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:58,665] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:58,668] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:58,668] [INFO] Target genome list was writen to GCF_008802145.1_ASM880214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:58,676] [INFO] Task started: fastANI
[2024-01-24 14:56:58,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5b22741-71f3-4808-a3eb-793ae5525b63/GCF_008802145.1_ASM880214v1_genomic.fna.gz --refList GCF_008802145.1_ASM880214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802145.1_ASM880214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:21,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:21,835] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:21,836] [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_902499115.1	s__Burkholderia diffusa	99.9951	2104	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.35	95.51	0.88	0.82	18	conclusive
GCF_001718315.1	s__Burkholderia diffusa_B	94.3079	1741	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.1139	98.43	98.33	0.91	0.89	12	-
GCF_000949135.2	s__Burkholderia sp000949135	93.7999	1728	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.23	98.18	0.87	0.85	15	-
GCF_902833055.1	s__Burkholderia territorii	93.7728	1697	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.1139	98.56	96.71	0.92	0.86	37	-
GCF_003853645.1	s__Burkholderia sp003853645	93.4833	1758	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.08	96.08	0.79	0.79	2	-
GCF_003853415.1	s__Burkholderia sp003853415	93.2554	1725	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.32	99.32	0.91	0.91	2	-
GCF_001443045.1	s__Burkholderia ambifaria_A	92.8966	1718	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.26	99.26	0.91	0.91	2	-
GCF_000292915.1	s__Burkholderia cepacia_D	92.8145	1552	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203915.1	s__Burkholderia ambifaria	92.719	1670	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.41	95.73	0.89	0.79	83	-
GCF_900446215.1	s__Burkholderia cenocepacia	90.9051	1640	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.1666	99.08	98.68	0.89	0.81	292	-
GCF_001411495.1	s__Burkholderia cepacia	90.8058	1717	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.84	96.33	0.89	0.79	182	-
GCF_001718835.1	s__Burkholderia cepacia_F	90.3461	1529	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:21,838] [INFO] GTDB search result was written to GCF_008802145.1_ASM880214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:21,839] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:21,843] [INFO] DFAST_QC result json was written to GCF_008802145.1_ASM880214v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:21,843] [INFO] DFAST_QC completed!
[2024-01-24 14:57:21,843] [INFO] Total running time: 0h2m13s