[2023-06-19 04:28:29,393] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:28:29,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:28:29,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference
[2023-06-19 04:28:31,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:28:31,140] [INFO] Task started: Prodigal
[2023-06-19 04:28:31,140] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbd3b3fe-73e4-487e-920d-0884d1a700f7/GCA_018003555.1_ASM1800355v1_genomic.fna.gz | prodigal -d GCA_018003555.1_ASM1800355v1_genomic.fna/cds.fna -a GCA_018003555.1_ASM1800355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:28:34,669] [INFO] Task succeeded: Prodigal
[2023-06-19 04:28:34,669] [INFO] Task started: HMMsearch
[2023-06-19 04:28:34,669] [INFO] Running command: hmmsearch --tblout GCA_018003555.1_ASM1800355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference/reference_markers.hmm GCA_018003555.1_ASM1800355v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:28:34,878] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:28:34,879] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdbd3b3fe-73e4-487e-920d-0884d1a700f7/GCA_018003555.1_ASM1800355v1_genomic.fna.gz]
[2023-06-19 04:28:34,908] [INFO] Query marker FASTA was written to GCA_018003555.1_ASM1800355v1_genomic.fna/markers.fasta
[2023-06-19 04:28:34,909] [INFO] Task started: Blastn
[2023-06-19 04:28:34,909] [INFO] Running command: blastn -query GCA_018003555.1_ASM1800355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference/reference_markers.fasta -out GCA_018003555.1_ASM1800355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:28:35,701] [INFO] Task succeeded: Blastn
[2023-06-19 04:28:35,704] [INFO] Selected 12 target genomes.
[2023-06-19 04:28:35,704] [INFO] Target genome list was writen to GCA_018003555.1_ASM1800355v1_genomic.fna/target_genomes.txt
[2023-06-19 04:28:35,707] [INFO] Task started: fastANI
[2023-06-19 04:28:35,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd3b3fe-73e4-487e-920d-0884d1a700f7/GCA_018003555.1_ASM1800355v1_genomic.fna.gz --refList GCA_018003555.1_ASM1800355v1_genomic.fna/target_genomes.txt --output GCA_018003555.1_ASM1800355v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:28:47,525] [INFO] Task succeeded: fastANI
[2023-06-19 04:28:47,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:28:47,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:28:47,538] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:28:47,539] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:28:47,539] [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
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	88.4028	266	280	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	87.5366	250	280	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	83.6398	226	280	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	83.5951	236	280	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	83.5233	224	280	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	83.3819	228	280	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	80.4763	174	280	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.577	156	280	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.5362	159	280	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.5304	142	280	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.3459	146	280	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.9871	145	280	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:28:47,547] [INFO] DFAST Taxonomy check result was written to GCA_018003555.1_ASM1800355v1_genomic.fna/tc_result.tsv
[2023-06-19 04:28:47,548] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:28:47,548] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:28:47,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference/checkm_data
[2023-06-19 04:28:47,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:28:47,574] [INFO] Task started: CheckM
[2023-06-19 04:28:47,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018003555.1_ASM1800355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018003555.1_ASM1800355v1_genomic.fna/checkm_input GCA_018003555.1_ASM1800355v1_genomic.fna/checkm_result
[2023-06-19 04:29:06,357] [INFO] Task succeeded: CheckM
[2023-06-19 04:29:06,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:29:06,381] [INFO] ===== Completeness check finished =====
[2023-06-19 04:29:06,381] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:29:06,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018003555.1_ASM1800355v1_genomic.fna/markers.fasta)
[2023-06-19 04:29:06,382] [INFO] Task started: Blastn
[2023-06-19 04:29:06,382] [INFO] Running command: blastn -query GCA_018003555.1_ASM1800355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdda3e18-30c1-48a6-a877-5a376950ccd3/dqc_reference/reference_markers_gtdb.fasta -out GCA_018003555.1_ASM1800355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:07,678] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:07,683] [INFO] Selected 11 target genomes.
[2023-06-19 04:29:07,683] [INFO] Target genome list was writen to GCA_018003555.1_ASM1800355v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:29:07,690] [INFO] Task started: fastANI
[2023-06-19 04:29:07,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd3b3fe-73e4-487e-920d-0884d1a700f7/GCA_018003555.1_ASM1800355v1_genomic.fna.gz --refList GCA_018003555.1_ASM1800355v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018003555.1_ASM1800355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:29:15,259] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:15,270] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:29:15,270] [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
GCA_003268905.1	s__Acidovorax defluvii	99.1368	279	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.35	96.64	0.82	0.75	12	conclusive
GCF_002157145.1	s__Acidovorax carolinensis	88.4028	266	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.15	97.05	0.89	0.88	4	-
GCF_002176815.1	s__Acidovorax sp002176815	88.1803	254	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCF_900107605.1	s__Acidovorax soli	87.5159	251	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCA_011620245.1	s__Acidovorax sp011620245	86.088	181	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175235.1	s__Acidovorax delafieldii_B	84.4418	234	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852545.1	s__Acidovorax sp003852545	83.9007	233	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204195.1	s__Acidovorax radicis	83.5233	224	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.28	97.43	0.95	0.93	5	-
GCF_000238595.1	s__Acidovorax facilis	83.3608	232	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCF_001422735.1	s__Acidovorax sp001422735	83.269	228	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424425.1	s__Acidovorax sp001424425	83.0366	232	280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2023-06-19 04:29:15,273] [INFO] GTDB search result was written to GCA_018003555.1_ASM1800355v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:29:15,273] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:29:15,277] [INFO] DFAST_QC result json was written to GCA_018003555.1_ASM1800355v1_genomic.fna/dqc_result.json
[2023-06-19 04:29:15,278] [INFO] DFAST_QC completed!
[2023-06-19 04:29:15,278] [INFO] Total running time: 0h0m46s