[2023-06-19 14:28:51,516] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:28:51,520] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:28:51,520] [INFO] DQC Reference Directory: /var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference
[2023-06-19 14:28:53,574] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:28:53,575] [INFO] Task started: Prodigal
[2023-06-19 14:28:53,576] [INFO] Running command: gunzip -c /var/lib/cwl/stge670a771-9a6b-45d3-9a35-a7fcea0b07ae/GCA_018814985.1_ASM1881498v1_genomic.fna.gz | prodigal -d GCA_018814985.1_ASM1881498v1_genomic.fna/cds.fna -a GCA_018814985.1_ASM1881498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:09,885] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:09,886] [INFO] Task started: HMMsearch
[2023-06-19 14:29:09,886] [INFO] Running command: hmmsearch --tblout GCA_018814985.1_ASM1881498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference/reference_markers.hmm GCA_018814985.1_ASM1881498v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:10,203] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:10,204] [INFO] Found 6/6 markers.
[2023-06-19 14:29:10,249] [INFO] Query marker FASTA was written to GCA_018814985.1_ASM1881498v1_genomic.fna/markers.fasta
[2023-06-19 14:29:10,250] [INFO] Task started: Blastn
[2023-06-19 14:29:10,250] [INFO] Running command: blastn -query GCA_018814985.1_ASM1881498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference/reference_markers.fasta -out GCA_018814985.1_ASM1881498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:11,125] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:11,132] [INFO] Selected 13 target genomes.
[2023-06-19 14:29:11,132] [INFO] Target genome list was writen to GCA_018814985.1_ASM1881498v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:11,138] [INFO] Task started: fastANI
[2023-06-19 14:29:11,138] [INFO] Running command: fastANI --query /var/lib/cwl/stge670a771-9a6b-45d3-9a35-a7fcea0b07ae/GCA_018814985.1_ASM1881498v1_genomic.fna.gz --refList GCA_018814985.1_ASM1881498v1_genomic.fna/target_genomes.txt --output GCA_018814985.1_ASM1881498v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:29:24,006] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:24,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:29:24,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:29:24,020] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:29:24,020] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:29:24,020] [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	85.3223	1049	1416	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	85.0941	1057	1416	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	84.854	1063	1416	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	84.8368	1052	1416	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	82.8995	685	1416	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	82.7146	734	1416	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	82.3648	751	1416	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.5681	704	1416	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.0243	657	1416	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.0722	467	1416	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.9312	409	1416	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.7013	470	1416	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.5496	466	1416	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:29:24,022] [INFO] DFAST Taxonomy check result was written to GCA_018814985.1_ASM1881498v1_genomic.fna/tc_result.tsv
[2023-06-19 14:29:24,023] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:29:24,023] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:29:24,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference/checkm_data
[2023-06-19 14:29:24,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:29:24,078] [INFO] Task started: CheckM
[2023-06-19 14:29:24,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018814985.1_ASM1881498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018814985.1_ASM1881498v1_genomic.fna/checkm_input GCA_018814985.1_ASM1881498v1_genomic.fna/checkm_result
[2023-06-19 14:30:13,729] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:13,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.85%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-19 14:30:13,761] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:13,762] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:13,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018814985.1_ASM1881498v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:13,762] [INFO] Task started: Blastn
[2023-06-19 14:30:13,762] [INFO] Running command: blastn -query GCA_018814985.1_ASM1881498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafa1c3d-0edd-46b9-b251-63a72f781540/dqc_reference/reference_markers_gtdb.fasta -out GCA_018814985.1_ASM1881498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:15,360] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:15,366] [INFO] Selected 20 target genomes.
[2023-06-19 14:30:15,366] [INFO] Target genome list was writen to GCA_018814985.1_ASM1881498v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:15,377] [INFO] Task started: fastANI
[2023-06-19 14:30:15,377] [INFO] Running command: fastANI --query /var/lib/cwl/stge670a771-9a6b-45d3-9a35-a7fcea0b07ae/GCA_018814985.1_ASM1881498v1_genomic.fna.gz --refList GCA_018814985.1_ASM1881498v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018814985.1_ASM1881498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:37,247] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:37,264] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:30:37,265] [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_018828125.1	s__Acidovorax sp018828125	98.6908	1339	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.50	98.69	0.98	0.93	11	conclusive
GCF_013376875.1	s__Acidovorax sp001411535	85.4138	1090	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.38	95.78	0.89	0.84	16	-
GCF_000204195.1	s__Acidovorax radicis	85.0941	1057	1416	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	84.8368	1052	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCF_003058055.1	s__Acidovorax sp003058055	84.7864	1013	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCA_018780365.1	s__Acidovorax sp018780365	84.7737	870	1416	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	84.7413	1055	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_000238595.1	s__Acidovorax facilis	84.7289	918	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCF_002797445.1	s__Acidovorax sp002797445	84.5652	993	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783915.1	s__Acidovorax sp016783915	84.5275	955	1416	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	83.9621	1056	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_001422735.1	s__Acidovorax sp001422735	83.9286	1050	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003208485.1	s__Acidovorax sp003208485	83.0652	986	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428665.1	s__Acidovorax sp001428665	82.9703	1023	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
GCF_900107605.1	s__Acidovorax soli	82.9096	684	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCF_003669015.1	s__Acidovorax sp002754495	82.874	862	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCF_003053545.1	s__Acidovorax sp003053545	82.8319	1015	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_013408765.1	s__Acidovorax sp013408765	82.8255	1026	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157145.1	s__Acidovorax carolinensis	82.7259	733	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.15	97.05	0.89	0.88	4	-
GCA_003268905.1	s__Acidovorax defluvii	82.6003	703	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.35	96.64	0.82	0.75	12	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:37,267] [INFO] GTDB search result was written to GCA_018814985.1_ASM1881498v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:37,268] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:37,274] [INFO] DFAST_QC result json was written to GCA_018814985.1_ASM1881498v1_genomic.fna/dqc_result.json
[2023-06-19 14:30:37,274] [INFO] DFAST_QC completed!
[2023-06-19 14:30:37,275] [INFO] Total running time: 0h1m46s