[2023-06-29 05:38:32,744] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:38:32,746] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:38:32,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference
[2023-06-29 05:38:33,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:38:33,988] [INFO] Task started: Prodigal
[2023-06-29 05:38:33,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgcae0d3a5-ca57-4a6b-8741-1853769488f7/GCA_020055795.1_ASM2005579v1_genomic.fna.gz | prodigal -d GCA_020055795.1_ASM2005579v1_genomic.fna/cds.fna -a GCA_020055795.1_ASM2005579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:38:44,135] [INFO] Task succeeded: Prodigal
[2023-06-29 05:38:44,135] [INFO] Task started: HMMsearch
[2023-06-29 05:38:44,136] [INFO] Running command: hmmsearch --tblout GCA_020055795.1_ASM2005579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference/reference_markers.hmm GCA_020055795.1_ASM2005579v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:38:44,391] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:38:44,392] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcae0d3a5-ca57-4a6b-8741-1853769488f7/GCA_020055795.1_ASM2005579v1_genomic.fna.gz]
[2023-06-29 05:38:44,431] [INFO] Query marker FASTA was written to GCA_020055795.1_ASM2005579v1_genomic.fna/markers.fasta
[2023-06-29 05:38:44,431] [INFO] Task started: Blastn
[2023-06-29 05:38:44,431] [INFO] Running command: blastn -query GCA_020055795.1_ASM2005579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference/reference_markers.fasta -out GCA_020055795.1_ASM2005579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:38:45,360] [INFO] Task succeeded: Blastn
[2023-06-29 05:38:45,365] [INFO] Selected 11 target genomes.
[2023-06-29 05:38:45,366] [INFO] Target genome list was writen to GCA_020055795.1_ASM2005579v1_genomic.fna/target_genomes.txt
[2023-06-29 05:38:45,367] [INFO] Task started: fastANI
[2023-06-29 05:38:45,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgcae0d3a5-ca57-4a6b-8741-1853769488f7/GCA_020055795.1_ASM2005579v1_genomic.fna.gz --refList GCA_020055795.1_ASM2005579v1_genomic.fna/target_genomes.txt --output GCA_020055795.1_ASM2005579v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:38:56,158] [INFO] Task succeeded: fastANI
[2023-06-29 05:38:56,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:38:56,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:38:56,174] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:38:56,174] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 05:38:56,174] [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
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	87.7446	505	785	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	87.5716	533	785	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	87.2014	432	785	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	86.9133	512	785	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	86.7737	495	785	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	83.9225	434	785	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	82.2747	294	785	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	82.105	315	785	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	81.5476	392	785	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.4867	349	785	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.0297	286	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 05:38:56,177] [INFO] DFAST Taxonomy check result was written to GCA_020055795.1_ASM2005579v1_genomic.fna/tc_result.tsv
[2023-06-29 05:38:56,177] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:38:56,177] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:38:56,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference/checkm_data
[2023-06-29 05:38:56,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:38:56,220] [INFO] Task started: CheckM
[2023-06-29 05:38:56,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020055795.1_ASM2005579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020055795.1_ASM2005579v1_genomic.fna/checkm_input GCA_020055795.1_ASM2005579v1_genomic.fna/checkm_result
[2023-06-29 05:39:30,199] [INFO] Task succeeded: CheckM
[2023-06-29 05:39:30,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 12.50%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 05:39:30,226] [INFO] ===== Completeness check finished =====
[2023-06-29 05:39:30,226] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:39:30,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020055795.1_ASM2005579v1_genomic.fna/markers.fasta)
[2023-06-29 05:39:30,227] [INFO] Task started: Blastn
[2023-06-29 05:39:30,227] [INFO] Running command: blastn -query GCA_020055795.1_ASM2005579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg446ef7c2-d6b1-44fc-a62b-4f72406aac01/dqc_reference/reference_markers_gtdb.fasta -out GCA_020055795.1_ASM2005579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:39:32,038] [INFO] Task succeeded: Blastn
[2023-06-29 05:39:32,044] [INFO] Selected 15 target genomes.
[2023-06-29 05:39:32,044] [INFO] Target genome list was writen to GCA_020055795.1_ASM2005579v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:39:32,058] [INFO] Task started: fastANI
[2023-06-29 05:39:32,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgcae0d3a5-ca57-4a6b-8741-1853769488f7/GCA_020055795.1_ASM2005579v1_genomic.fna.gz --refList GCA_020055795.1_ASM2005579v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020055795.1_ASM2005579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:39:49,271] [INFO] Task succeeded: fastANI
[2023-06-29 05:39:49,288] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 05:39:49,288] [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_016806145.1	s__Variovorax sp900115375	94.7198	691	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCF_003053685.1	s__Variovorax sp003053685	87.8701	523	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	100.00	100.00	1.00	1.00	5	-
GCF_013376045.1	s__Variovorax sp013376045	87.8639	512	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591345.1	s__Variovorax boronicumulans	87.7443	505	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	97.15	97.07	0.92	0.90	8	-
GCF_003952185.1	s__Variovorax sp003952185	87.6383	515	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.99	99.98	0.99	0.99	3	-
GCF_000382045.1	s__Variovorax paradoxus_A	87.617	542	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCF_003952165.1	s__Variovorax guangxiensis	87.5715	533	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	97.91	97.91	0.87	0.87	2	-
GCF_004216615.1	s__Variovorax sp004216615	87.5511	516	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003019815.1	s__Variovorax sp003019815	87.4957	528	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.10	98.33	0.94	0.92	3	-
GCF_001425205.1	s__Variovorax sp001425205	87.29	474	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828835.1	s__Variovorax beijingensis_A	86.7443	503	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.17	99.08	0.93	0.90	4	-
GCF_018614955.1	s__Variovorax paradoxus_J	85.0841	441	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003984645.1	s__Variovorax sp003984645	85.0721	418	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101545.1	s__Variovorax sp900101545	84.9877	443	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211245.1	s__Variovorax sp004211245	83.082	315	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 05:39:49,290] [INFO] GTDB search result was written to GCA_020055795.1_ASM2005579v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:39:49,290] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:39:49,294] [INFO] DFAST_QC result json was written to GCA_020055795.1_ASM2005579v1_genomic.fna/dqc_result.json
[2023-06-29 05:39:49,294] [INFO] DFAST_QC completed!
[2023-06-29 05:39:49,294] [INFO] Total running time: 0h1m17s