[2024-01-24 15:18:27,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference
[2024-01-24 15:18:28,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,812] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e67a043-355d-444a-b4d0-b776c238e08e/GCF_009646335.1_ASM964633v1_genomic.fna.gz | prodigal -d GCF_009646335.1_ASM964633v1_genomic.fna/cds.fna -a GCF_009646335.1_ASM964633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:47,100] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:47,101] [INFO] Task started: HMMsearch
[2024-01-24 15:18:47,101] [INFO] Running command: hmmsearch --tblout GCF_009646335.1_ASM964633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference/reference_markers.hmm GCF_009646335.1_ASM964633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:47,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:47,427] [INFO] Found 6/6 markers.
[2024-01-24 15:18:47,470] [INFO] Query marker FASTA was written to GCF_009646335.1_ASM964633v1_genomic.fna/markers.fasta
[2024-01-24 15:18:47,471] [INFO] Task started: Blastn
[2024-01-24 15:18:47,471] [INFO] Running command: blastn -query GCF_009646335.1_ASM964633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference/reference_markers.fasta -out GCF_009646335.1_ASM964633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:48,399] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:48,404] [INFO] Selected 21 target genomes.
[2024-01-24 15:18:48,405] [INFO] Target genome list was writen to GCF_009646335.1_ASM964633v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:48,415] [INFO] Task started: fastANI
[2024-01-24 15:18:48,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e67a043-355d-444a-b4d0-b776c238e08e/GCF_009646335.1_ASM964633v1_genomic.fna.gz --refList GCF_009646335.1_ASM964633v1_genomic.fna/target_genomes.txt --output GCF_009646335.1_ASM964633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:11,213] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:11,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:11,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:11,233] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:11,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:11,234] [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
Caenimonas koreensis	strain=EMB320	GCA_009646335.1	367474	367474	type	True	100.0	1512	1515	95	conclusive
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.1594	673	1515	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	79.907	591	1515	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	79.8629	634	1515	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	79.7352	629	1515	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.7213	616	1515	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.697	645	1515	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.5535	593	1515	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	79.5488	593	1515	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.5244	688	1515	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	79.5024	623	1515	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	79.4793	677	1515	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.4203	593	1515	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	79.2422	540	1515	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	79.2277	539	1515	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.0718	506	1515	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.8762	542	1515	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.8269	500	1515	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	78.6738	453	1515	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.6586	452	1515	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.8111	347	1515	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:11,238] [INFO] DFAST Taxonomy check result was written to GCF_009646335.1_ASM964633v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:11,239] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:11,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:11,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference/checkm_data
[2024-01-24 15:19:11,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:11,288] [INFO] Task started: CheckM
[2024-01-24 15:19:11,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009646335.1_ASM964633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009646335.1_ASM964633v1_genomic.fna/checkm_input GCF_009646335.1_ASM964633v1_genomic.fna/checkm_result
[2024-01-24 15:20:16,838] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:16,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:16,860] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:16,860] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:16,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009646335.1_ASM964633v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:16,861] [INFO] Task started: Blastn
[2024-01-24 15:20:16,861] [INFO] Running command: blastn -query GCF_009646335.1_ASM964633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac66f980-c373-4443-8ec7-ea96b23dc108/dqc_reference/reference_markers_gtdb.fasta -out GCF_009646335.1_ASM964633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:18,514] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:18,518] [INFO] Selected 17 target genomes.
[2024-01-24 15:20:18,518] [INFO] Target genome list was writen to GCF_009646335.1_ASM964633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:18,531] [INFO] Task started: fastANI
[2024-01-24 15:20:18,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e67a043-355d-444a-b4d0-b776c238e08e/GCF_009646335.1_ASM964633v1_genomic.fna.gz --refList GCF_009646335.1_ASM964633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009646335.1_ASM964633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:37,270] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:37,288] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:37,288] [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_009646335.1	s__Ramlibacter koreensis	100.0	1511	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015831345.1	s__Ramlibacter sp015831345	80.789	758	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044395.1	s__Ramlibacter sp001044395	80.6566	801	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191525.1	s__Ramlibacter sp016191525	80.5119	728	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797765.1	s__Ramlibacter sp003797765	80.4513	776	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155545.1	s__Ramlibacter soli	80.1757	698	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	80.0655	679	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	80.0358	665	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000426125.1	s__Ramlibacter sp000426125	79.7015	645	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815685.1	s__Ramlibacter sp013815685	79.692	583	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833165.1	s__Ramlibacter sp007833165	79.6705	698	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427815.1	s__Ramlibacter tataouinensis_A	79.5269	577	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.98	0.97	3	-
GCF_001426505.1	s__Variovorax sp001426505	79.4076	593	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115685.1	s__Variovorax sp900115685	79.3024	622	1515	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	79.1928	586	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806145.1	s__Variovorax sp900115375	79.074	619	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCF_900114785.1	s__Variovorax sp900114785	79.0653	567	1515	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 15:20:37,295] [INFO] GTDB search result was written to GCF_009646335.1_ASM964633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:37,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:37,300] [INFO] DFAST_QC result json was written to GCF_009646335.1_ASM964633v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:37,300] [INFO] DFAST_QC completed!
[2024-01-24 15:20:37,300] [INFO] Total running time: 0h2m10s