[2023-06-18 11:25:41,324] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:25:41,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:25:41,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference
[2023-06-18 11:25:43,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:25:43,612] [INFO] Task started: Prodigal
[2023-06-18 11:25:43,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg5024b31e-bd65-4ea5-8b81-78dd42d78539/GCA_018607085.1_ASM1860708v1_genomic.fna.gz | prodigal -d GCA_018607085.1_ASM1860708v1_genomic.fna/cds.fna -a GCA_018607085.1_ASM1860708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:25:52,037] [INFO] Task succeeded: Prodigal
[2023-06-18 11:25:52,037] [INFO] Task started: HMMsearch
[2023-06-18 11:25:52,037] [INFO] Running command: hmmsearch --tblout GCA_018607085.1_ASM1860708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference/reference_markers.hmm GCA_018607085.1_ASM1860708v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:25:52,337] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:25:52,338] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5024b31e-bd65-4ea5-8b81-78dd42d78539/GCA_018607085.1_ASM1860708v1_genomic.fna.gz]
[2023-06-18 11:25:52,370] [INFO] Query marker FASTA was written to GCA_018607085.1_ASM1860708v1_genomic.fna/markers.fasta
[2023-06-18 11:25:52,371] [INFO] Task started: Blastn
[2023-06-18 11:25:52,371] [INFO] Running command: blastn -query GCA_018607085.1_ASM1860708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference/reference_markers.fasta -out GCA_018607085.1_ASM1860708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:25:53,211] [INFO] Task succeeded: Blastn
[2023-06-18 11:25:53,215] [INFO] Selected 35 target genomes.
[2023-06-18 11:25:53,216] [INFO] Target genome list was writen to GCA_018607085.1_ASM1860708v1_genomic.fna/target_genomes.txt
[2023-06-18 11:25:53,224] [INFO] Task started: fastANI
[2023-06-18 11:25:53,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg5024b31e-bd65-4ea5-8b81-78dd42d78539/GCA_018607085.1_ASM1860708v1_genomic.fna.gz --refList GCA_018607085.1_ASM1860708v1_genomic.fna/target_genomes.txt --output GCA_018607085.1_ASM1860708v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:26:15,950] [INFO] Task succeeded: fastANI
[2023-06-18 11:26:15,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:26:15,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:26:15,973] [INFO] Found 23 fastANI hits (8 hits with ANI > threshold)
[2023-06-18 11:26:15,973] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-18 11:26:15,974] [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
Vaginimicrobium propionicum	strain=Marseille-P3275	GCA_900155645.1	1871034	1871034	type	True	97.5279	139	1083	95	inconclusive
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	97.0962	171	1083	95	inconclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.0654	184	1083	95	inconclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	96.8967	176	1083	95	inconclusive
Alloscardovia omnicolens	strain=DSM 21503	GCA_000420505.1	419015	419015	type	True	96.8741	50	1083	95	inconclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	96.6677	174	1083	95	inconclusive
Burkholderia contaminans	strain=LMG 23361	GCA_000987075.1	488447	488447	type	True	96.0402	340	1083	95	inconclusive
Burkholderia contaminans	strain=LMG 23361	GCA_001758385.2	488447	488447	type	True	96.0113	344	1083	95	inconclusive
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	93.9611	85	1083	95	below_threshold
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	93.4661	81	1083	95	below_threshold
Burkholderia lata	strain=383	GCA_000012945.1	482957	482957	suspected-type	True	91.595	297	1083	95	below_threshold
Burkholderia puraquae	strain=CAMPA 1040	GCA_002099195.1	1904757	1904757	type	True	90.8873	312	1083	95	below_threshold
Burkholderia aenigmatica	strain=LMG 13014	GCA_902499175.1	2015348	2015348	suspected-type	True	89.6365	284	1083	95	below_threshold
Burkholderia metallica	strain=LMG 24068	GCA_902832845.1	488729	488729	type	True	89.1843	263	1083	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	87.7916	267	1083	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	86.9308	249	1083	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	85.6824	250	1083	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	85.4651	248	1083	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	81.9528	133	1083	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	81.9482	194	1083	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.0577	127	1083	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	79.9241	188	1083	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.9577	86	1083	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:26:15,976] [INFO] DFAST Taxonomy check result was written to GCA_018607085.1_ASM1860708v1_genomic.fna/tc_result.tsv
[2023-06-18 11:26:15,976] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:26:15,977] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:26:15,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference/checkm_data
[2023-06-18 11:26:15,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:26:16,018] [INFO] Task started: CheckM
[2023-06-18 11:26:16,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607085.1_ASM1860708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607085.1_ASM1860708v1_genomic.fna/checkm_input GCA_018607085.1_ASM1860708v1_genomic.fna/checkm_result
[2023-06-18 11:26:45,850] [INFO] Task succeeded: CheckM
[2023-06-18 11:26:45,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:26:45,875] [INFO] ===== Completeness check finished =====
[2023-06-18 11:26:45,875] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:26:45,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607085.1_ASM1860708v1_genomic.fna/markers.fasta)
[2023-06-18 11:26:45,876] [INFO] Task started: Blastn
[2023-06-18 11:26:45,876] [INFO] Running command: blastn -query GCA_018607085.1_ASM1860708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55321e12-4c40-49bd-b6bf-abfe7a6224a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607085.1_ASM1860708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:26:47,288] [INFO] Task succeeded: Blastn
[2023-06-18 11:26:47,294] [INFO] Selected 27 target genomes.
[2023-06-18 11:26:47,294] [INFO] Target genome list was writen to GCA_018607085.1_ASM1860708v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:26:47,334] [INFO] Task started: fastANI
[2023-06-18 11:26:47,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg5024b31e-bd65-4ea5-8b81-78dd42d78539/GCA_018607085.1_ASM1860708v1_genomic.fna.gz --refList GCA_018607085.1_ASM1860708v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607085.1_ASM1860708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:27:03,811] [INFO] Task succeeded: fastANI
[2023-06-18 11:27:03,830] [INFO] Found 18 fastANI hits (4 hits with ANI > circumscription radius)
[2023-06-18 11:27:03,830] [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_900155645.1	s__Propionimicrobium sp900155645	97.5279	139	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionimicrobium	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_018987235.1	s__Lactobacillus crispatus	96.9459	185	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	inconclusive
GCF_000420505.1	s__Alloscardovia omnicolens	96.8741	50	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	98.68	97.50	0.93	0.88	12	inconclusive
GCF_000987075.1	s__Burkholderia contaminans	96.0402	340	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.97	95.20	0.90	0.82	86	inconclusive
GCF_000160875.1	s__Lactobacillus iners	93.9611	85	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	-
GCF_000012945.1	s__Burkholderia lata	91.595	297	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.57	95.30	0.88	0.82	11	-
GCF_902499335.1	s__Burkholderia lata_B	91.0843	307	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.27	95.15	0.87	0.83	7	-
GCF_902833045.1	s__Burkholderia sp902833045	90.1598	293	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.81	96.81	0.81	0.81	2	-
GCF_902499175.1	s__Burkholderia aenigmatica	89.6365	284	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.89	95.59	0.85	0.80	12	-
GCF_902832845.1	s__Burkholderia metallica	89.1909	264	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.19	98.00	0.94	0.86	6	-
GCF_001718835.1	s__Burkholderia cepacia_F	88.4751	258	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001522585.2	s__Burkholderia sp001522585	87.8303	266	1083	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.44	95.03	0.88	0.83	18	-
GCF_000615285.1	s__Lactobacillus kitasatonis	82.5942	122	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001434975.1	s__Lactobacillus gallinarum	81.8024	136	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000160855.1	s__Lactobacillus helveticus	81.6551	126	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_002706375.1	s__Lactobacillus amylovorus	81.5827	141	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.1448	125	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_001591845.1	s__Lactobacillus acidophilus	81.0364	127	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
--------------------------------------------------------------------------------
[2023-06-18 11:27:03,832] [INFO] GTDB search result was written to GCA_018607085.1_ASM1860708v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:27:03,833] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:27:03,837] [INFO] DFAST_QC result json was written to GCA_018607085.1_ASM1860708v1_genomic.fna/dqc_result.json
[2023-06-18 11:27:03,838] [INFO] DFAST_QC completed!
[2023-06-18 11:27:03,838] [INFO] Total running time: 0h1m23s