[2023-06-18 22:24:41,787] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:24:41,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:24:41,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference
[2023-06-18 22:24:42,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:24:42,932] [INFO] Task started: Prodigal
[2023-06-18 22:24:42,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg536da39f-5d2f-490d-921e-b469a912fc01/GCA_018820875.1_ASM1882087v1_genomic.fna.gz | prodigal -d GCA_018820875.1_ASM1882087v1_genomic.fna/cds.fna -a GCA_018820875.1_ASM1882087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:24:57,806] [INFO] Task succeeded: Prodigal
[2023-06-18 22:24:57,806] [INFO] Task started: HMMsearch
[2023-06-18 22:24:57,806] [INFO] Running command: hmmsearch --tblout GCA_018820875.1_ASM1882087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference/reference_markers.hmm GCA_018820875.1_ASM1882087v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:24:58,047] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:24:58,048] [INFO] Found 6/6 markers.
[2023-06-18 22:24:58,090] [INFO] Query marker FASTA was written to GCA_018820875.1_ASM1882087v1_genomic.fna/markers.fasta
[2023-06-18 22:24:58,090] [INFO] Task started: Blastn
[2023-06-18 22:24:58,091] [INFO] Running command: blastn -query GCA_018820875.1_ASM1882087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference/reference_markers.fasta -out GCA_018820875.1_ASM1882087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:24:58,972] [INFO] Task succeeded: Blastn
[2023-06-18 22:24:58,978] [INFO] Selected 17 target genomes.
[2023-06-18 22:24:58,978] [INFO] Target genome list was writen to GCA_018820875.1_ASM1882087v1_genomic.fna/target_genomes.txt
[2023-06-18 22:24:58,980] [INFO] Task started: fastANI
[2023-06-18 22:24:58,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg536da39f-5d2f-490d-921e-b469a912fc01/GCA_018820875.1_ASM1882087v1_genomic.fna.gz --refList GCA_018820875.1_ASM1882087v1_genomic.fna/target_genomes.txt --output GCA_018820875.1_ASM1882087v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:25:16,135] [INFO] Task succeeded: fastANI
[2023-06-18 22:25:16,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:25:16,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:25:16,149] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:25:16,149] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:25:16,149] [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 paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	81.9017	856	1565	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	81.8891	856	1565	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	81.4535	797	1565	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	81.3679	848	1565	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	81.2986	687	1565	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	80.6809	747	1565	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.351	527	1565	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.2179	476	1565	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0449	572	1565	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.0035	524	1565	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	78.9509	490	1565	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.9225	535	1565	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	78.9025	510	1565	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	78.8891	504	1565	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	78.7707	495	1565	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.7106	620	1565	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	78.2702	335	1565	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:25:16,153] [INFO] DFAST Taxonomy check result was written to GCA_018820875.1_ASM1882087v1_genomic.fna/tc_result.tsv
[2023-06-18 22:25:16,153] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:25:16,153] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:25:16,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference/checkm_data
[2023-06-18 22:25:16,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:25:16,201] [INFO] Task started: CheckM
[2023-06-18 22:25:16,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018820875.1_ASM1882087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018820875.1_ASM1882087v1_genomic.fna/checkm_input GCA_018820875.1_ASM1882087v1_genomic.fna/checkm_result
[2023-06-18 22:26:14,619] [INFO] Task succeeded: CheckM
[2023-06-18 22:26:14,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 7.45%
Strain heterogeneity: 22.22%
--------------------------------------------------------------------------------
[2023-06-18 22:26:14,647] [INFO] ===== Completeness check finished =====
[2023-06-18 22:26:14,647] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:26:14,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018820875.1_ASM1882087v1_genomic.fna/markers.fasta)
[2023-06-18 22:26:14,647] [INFO] Task started: Blastn
[2023-06-18 22:26:14,648] [INFO] Running command: blastn -query GCA_018820875.1_ASM1882087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7c2aa7-226d-4c8e-8f6e-6faea6305fa1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018820875.1_ASM1882087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:26:16,336] [INFO] Task succeeded: Blastn
[2023-06-18 22:26:16,342] [INFO] Selected 17 target genomes.
[2023-06-18 22:26:16,342] [INFO] Target genome list was writen to GCA_018820875.1_ASM1882087v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:26:16,350] [INFO] Task started: fastANI
[2023-06-18 22:26:16,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg536da39f-5d2f-490d-921e-b469a912fc01/GCA_018820875.1_ASM1882087v1_genomic.fna.gz --refList GCA_018820875.1_ASM1882087v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018820875.1_ASM1882087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:26:36,840] [INFO] Task succeeded: fastANI
[2023-06-18 22:26:36,855] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:26:36,855] [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_018820395.1	s__Variovorax sp018820395	99.8298	1467	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.74	99.65	0.94	0.94	3	conclusive
GCF_018614955.1	s__Variovorax paradoxus_J	82.4251	854	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614915.1	s__Variovorax paradoxus_K	82.4006	840	1565	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	82.3531	844	1565	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	82.2857	872	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901827185.1	s__Variovorax sp901827185	82.1161	861	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.21	98.21	0.91	0.91	2	-
GCF_009765735.1	s__Variovorax sp009765735	81.6635	805	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000463015.1	s__Variovorax paradoxus_E	81.62	878	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.39	98.39	0.87	0.87	2	-
GCF_901827175.1	s__Variovorax sp901827175	81.606	859	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170375.1	s__Variovorax sp014170375	81.5225	789	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282635.1	s__Variovorax sp000282635	81.3759	793	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.21	96.21	0.87	0.87	2	-
GCA_001899795.1	s__Variovorax sp001899795	81.3422	864	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.99	99.99	0.99	0.98	4	-
GCF_017161115.1	s__Variovorax sp017161115	81.3246	850	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754375.1	s__Variovorax sp002754375	81.3128	818	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	95.39	95.37	0.86	0.85	3	-
GCF_900115685.1	s__Variovorax sp900115685	81.2241	869	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184745.1	s__Variovorax paradoxus_C	81.211	840	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577265.1	s__Variovorax sp001577265	80.8394	744	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:26:36,857] [INFO] GTDB search result was written to GCA_018820875.1_ASM1882087v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:26:36,858] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:26:36,862] [INFO] DFAST_QC result json was written to GCA_018820875.1_ASM1882087v1_genomic.fna/dqc_result.json
[2023-06-18 22:26:36,862] [INFO] DFAST_QC completed!
[2023-06-18 22:26:36,862] [INFO] Total running time: 0h1m55s