[2024-01-24 10:57:13,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference
[2024-01-24 10:57:14,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,635] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg77ccdf8d-650c-407d-adff-bf4012d133be/GCF_023913775.1_ASM2391377v1_genomic.fna.gz | prodigal -d GCF_023913775.1_ASM2391377v1_genomic.fna/cds.fna -a GCF_023913775.1_ASM2391377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,595] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,595] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,595] [INFO] Running command: hmmsearch --tblout GCF_023913775.1_ASM2391377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference/reference_markers.hmm GCF_023913775.1_ASM2391377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:37,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:37,027] [INFO] Found 6/6 markers.
[2024-01-24 10:57:37,108] [INFO] Query marker FASTA was written to GCF_023913775.1_ASM2391377v1_genomic.fna/markers.fasta
[2024-01-24 10:57:37,109] [INFO] Task started: Blastn
[2024-01-24 10:57:37,109] [INFO] Running command: blastn -query GCF_023913775.1_ASM2391377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference/reference_markers.fasta -out GCF_023913775.1_ASM2391377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:38,173] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:38,176] [INFO] Selected 12 target genomes.
[2024-01-24 10:57:38,176] [INFO] Target genome list was writen to GCF_023913775.1_ASM2391377v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:38,181] [INFO] Task started: fastANI
[2024-01-24 10:57:38,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg77ccdf8d-650c-407d-adff-bf4012d133be/GCF_023913775.1_ASM2391377v1_genomic.fna.gz --refList GCF_023913775.1_ASM2391377v1_genomic.fna/target_genomes.txt --output GCF_023913775.1_ASM2391377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:54,212] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:54,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:54,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:54,224] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:54,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:54,225] [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 facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	100.0	1960	1975	95	conclusive
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	89.7042	1398	1975	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	88.1537	1296	1975	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	88.0899	1314	1975	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	84.4701	862	1975	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	83.9518	928	1975	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	83.7389	955	1975	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	81.4609	865	1975	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.5576	593	1975	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	79.4825	568	1975	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.261	553	1975	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.0781	655	1975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:54,226] [INFO] DFAST Taxonomy check result was written to GCF_023913775.1_ASM2391377v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:54,227] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:54,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:54,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference/checkm_data
[2024-01-24 10:57:54,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:54,294] [INFO] Task started: CheckM
[2024-01-24 10:57:54,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023913775.1_ASM2391377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023913775.1_ASM2391377v1_genomic.fna/checkm_input GCF_023913775.1_ASM2391377v1_genomic.fna/checkm_result
[2024-01-24 10:59:08,017] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:08,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:08,041] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:08,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:08,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023913775.1_ASM2391377v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:08,042] [INFO] Task started: Blastn
[2024-01-24 10:59:08,042] [INFO] Running command: blastn -query GCF_023913775.1_ASM2391377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc39ee6ef-045f-4234-b4ba-7d2655bfe74b/dqc_reference/reference_markers_gtdb.fasta -out GCF_023913775.1_ASM2391377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:10,113] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:10,130] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:10,131] [INFO] Target genome list was writen to GCF_023913775.1_ASM2391377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:10,159] [INFO] Task started: fastANI
[2024-01-24 10:59:10,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg77ccdf8d-650c-407d-adff-bf4012d133be/GCF_023913775.1_ASM2391377v1_genomic.fna.gz --refList GCF_023913775.1_ASM2391377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023913775.1_ASM2391377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:30,008] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:30,026] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:30,026] [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_013376875.1	s__Acidovorax sp001411535	96.3654	1540	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.38	95.78	0.89	0.84	16	conclusive
GCF_000204195.1	s__Acidovorax radicis	89.7041	1398	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.28	97.43	0.95	0.93	5	-
GCF_007993815.1	s__Acidovorax delafieldii	88.1537	1296	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCF_002245625.1	s__Acidovorax kalamii	88.0888	1314	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238595.1	s__Acidovorax facilis	87.8883	1133	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCA_016783915.1	s__Acidovorax sp016783915	87.628	1162	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	87.5028	1339	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCA_018780365.1	s__Acidovorax sp018780365	87.4187	1039	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302535.1	s__Acidovorax sp000302535	87.3148	1270	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.71	95.42	0.83	0.75	7	-
GCF_003058055.1	s__Acidovorax sp003058055	87.2261	1270	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCF_002797445.1	s__Acidovorax sp002797445	86.0692	1211	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107605.1	s__Acidovorax soli	84.4813	862	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCA_003208485.1	s__Acidovorax sp003208485	84.2875	1184	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	84.1095	1220	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_000175235.1	s__Acidovorax delafieldii_B	83.5236	793	1975	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:30,027] [INFO] GTDB search result was written to GCF_023913775.1_ASM2391377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:30,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:30,031] [INFO] DFAST_QC result json was written to GCF_023913775.1_ASM2391377v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:30,031] [INFO] DFAST_QC completed!
[2024-01-24 10:59:30,031] [INFO] Total running time: 0h2m17s