[2024-01-24 11:27:19,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference
[2024-01-24 11:27:20,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,375] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg2295092a-c176-4004-a7f9-258e08da4e4c/GCF_003951285.1_ASM395128v1_genomic.fna.gz | prodigal -d GCF_003951285.1_ASM395128v1_genomic.fna/cds.fna -a GCF_003951285.1_ASM395128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:42,262] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:42,263] [INFO] Task started: HMMsearch
[2024-01-24 11:27:42,263] [INFO] Running command: hmmsearch --tblout GCF_003951285.1_ASM395128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference/reference_markers.hmm GCF_003951285.1_ASM395128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:42,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:42,602] [INFO] Found 6/6 markers.
[2024-01-24 11:27:42,654] [INFO] Query marker FASTA was written to GCF_003951285.1_ASM395128v1_genomic.fna/markers.fasta
[2024-01-24 11:27:42,655] [INFO] Task started: Blastn
[2024-01-24 11:27:42,655] [INFO] Running command: blastn -query GCF_003951285.1_ASM395128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference/reference_markers.fasta -out GCF_003951285.1_ASM395128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:43,717] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:43,720] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:43,720] [INFO] Target genome list was writen to GCF_003951285.1_ASM395128v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:43,726] [INFO] Task started: fastANI
[2024-01-24 11:27:43,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg2295092a-c176-4004-a7f9-258e08da4e4c/GCF_003951285.1_ASM395128v1_genomic.fna.gz --refList GCF_003951285.1_ASM395128v1_genomic.fna/target_genomes.txt --output GCF_003951285.1_ASM395128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:28:02,203] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:02,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:28:02,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:28:02,219] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:28:02,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:28:02,220] [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 beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	100.0	2198	2212	95	conclusive
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	94.9031	1798	2212	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	87.9521	1388	2212	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	87.4353	1525	2212	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	87.0421	1266	2212	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	83.4026	1117	2212	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	81.1143	1058	2212	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.0768	781	2212	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.9581	772	2212	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.7146	759	2212	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.6735	840	2212	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.279	938	2212	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.8095	745	2212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:28:02,221] [INFO] DFAST Taxonomy check result was written to GCF_003951285.1_ASM395128v1_genomic.fna/tc_result.tsv
[2024-01-24 11:28:02,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:28:02,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:28:02,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference/checkm_data
[2024-01-24 11:28:02,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:28:02,288] [INFO] Task started: CheckM
[2024-01-24 11:28:02,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003951285.1_ASM395128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003951285.1_ASM395128v1_genomic.fna/checkm_input GCF_003951285.1_ASM395128v1_genomic.fna/checkm_result
[2024-01-24 11:29:46,711] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:46,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:46,730] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:46,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:46,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003951285.1_ASM395128v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:46,731] [INFO] Task started: Blastn
[2024-01-24 11:29:46,731] [INFO] Running command: blastn -query GCF_003951285.1_ASM395128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df9508f-bb13-4559-a50e-b32b1ce4abed/dqc_reference/reference_markers_gtdb.fasta -out GCF_003951285.1_ASM395128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:48,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:48,899] [INFO] Selected 8 target genomes.
[2024-01-24 11:29:48,899] [INFO] Target genome list was writen to GCF_003951285.1_ASM395128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:48,907] [INFO] Task started: fastANI
[2024-01-24 11:29:48,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg2295092a-c176-4004-a7f9-258e08da4e4c/GCF_003951285.1_ASM395128v1_genomic.fna.gz --refList GCF_003951285.1_ASM395128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003951285.1_ASM395128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:03,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:03,337] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:30:03,337] [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_003951285.1	s__Variovorax beijingensis	100.0	2198	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.27	99.27	0.92	0.92	2	conclusive
GCF_001591365.1	s__Variovorax paradoxus	94.9031	1798	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.93	98.38	0.94	0.90	4	-
GCF_000463015.1	s__Variovorax paradoxus_E	94.3789	1888	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.39	98.39	0.87	0.87	2	-
GCF_007828835.1	s__Variovorax beijingensis_A	94.3432	1856	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.17	99.08	0.93	0.90	4	-
GCF_018614875.1	s__Variovorax paradoxus_I	91.8187	1474	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003984625.1	s__Variovorax sp003984625	89.8219	1430	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000834655.1	s__Variovorax paradoxus_F	87.8373	1453	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161115.1	s__Variovorax sp017161115	87.7924	1526	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:30:03,338] [INFO] GTDB search result was written to GCF_003951285.1_ASM395128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:03,339] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:03,342] [INFO] DFAST_QC result json was written to GCF_003951285.1_ASM395128v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:03,342] [INFO] DFAST_QC completed!
[2024-01-24 11:30:03,342] [INFO] Total running time: 0h2m44s