[2024-01-25 18:40:20,737] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:20,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:20,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference
[2024-01-25 18:40:21,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:21,857] [INFO] Task started: Prodigal
[2024-01-25 18:40:21,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg49b276bd-6410-40af-8257-ec4eaec429d7/GCF_023721835.1_ASM2372183v1_genomic.fna.gz | prodigal -d GCF_023721835.1_ASM2372183v1_genomic.fna/cds.fna -a GCF_023721835.1_ASM2372183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:39,128] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:39,129] [INFO] Task started: HMMsearch
[2024-01-25 18:40:39,129] [INFO] Running command: hmmsearch --tblout GCF_023721835.1_ASM2372183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference/reference_markers.hmm GCF_023721835.1_ASM2372183v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:39,410] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:39,411] [INFO] Found 6/6 markers.
[2024-01-25 18:40:39,457] [INFO] Query marker FASTA was written to GCF_023721835.1_ASM2372183v1_genomic.fna/markers.fasta
[2024-01-25 18:40:39,458] [INFO] Task started: Blastn
[2024-01-25 18:40:39,458] [INFO] Running command: blastn -query GCF_023721835.1_ASM2372183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference/reference_markers.fasta -out GCF_023721835.1_ASM2372183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:40,488] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:40,491] [INFO] Selected 13 target genomes.
[2024-01-25 18:40:40,491] [INFO] Target genome list was writen to GCF_023721835.1_ASM2372183v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:40,495] [INFO] Task started: fastANI
[2024-01-25 18:40:40,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b276bd-6410-40af-8257-ec4eaec429d7/GCF_023721835.1_ASM2372183v1_genomic.fna.gz --refList GCF_023721835.1_ASM2372183v1_genomic.fna/target_genomes.txt --output GCF_023721835.1_ASM2372183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:53,578] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:53,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:53,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:53,587] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:40:53,587] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:40:53,588] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	84.1192	968	1815	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	84.0842	981	1815	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	84.0157	1004	1815	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	81.5452	924	1815	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.9596	615	1815	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.5309	620	1815	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.5133	613	1815	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.3755	570	1815	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.3005	695	1815	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.2277	510	1815	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.1918	736	1815	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.0627	580	1815	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.9204	520	1815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:53,589] [INFO] DFAST Taxonomy check result was written to GCF_023721835.1_ASM2372183v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:53,590] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:53,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:53,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference/checkm_data
[2024-01-25 18:40:53,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:53,642] [INFO] Task started: CheckM
[2024-01-25 18:40:53,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023721835.1_ASM2372183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023721835.1_ASM2372183v1_genomic.fna/checkm_input GCF_023721835.1_ASM2372183v1_genomic.fna/checkm_result
[2024-01-25 18:42:28,042] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:28,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:28,066] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:28,067] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:28,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023721835.1_ASM2372183v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:28,068] [INFO] Task started: Blastn
[2024-01-25 18:42:28,068] [INFO] Running command: blastn -query GCF_023721835.1_ASM2372183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf502b15f-03a5-4da4-90e7-0429569d92b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_023721835.1_ASM2372183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:30,239] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:30,242] [INFO] Selected 17 target genomes.
[2024-01-25 18:42:30,242] [INFO] Target genome list was writen to GCF_023721835.1_ASM2372183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:30,252] [INFO] Task started: fastANI
[2024-01-25 18:42:30,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b276bd-6410-40af-8257-ec4eaec429d7/GCF_023721835.1_ASM2372183v1_genomic.fna.gz --refList GCF_023721835.1_ASM2372183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023721835.1_ASM2372183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:50,182] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:50,192] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:42:50,192] [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_015476235.1	s__Schlegelella thermodepolymerans	84.0044	1005	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCA_001017435.1	s__Polyangium_A brachysporum	81.5195	928	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polyangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	81.121	789	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930615.1	s__Zhizhongheella caldifontis	80.7401	708	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Zhizhongheella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	80.7168	839	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	80.5511	833	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	80.4292	818	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	80.4264	806	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217215.1	s__Rivibacter subsaxonicus	80.1427	663	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	79.9332	716	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884255.1	s__VBDL01 sp005884255	79.8852	454	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219375.1	s__Aquabacterium sp016219375	79.8142	571	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	79.5884	672	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_903938815.1	s__Rubrivivax sp903938815	79.4441	591	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCF_900113225.1	s__Mitsuaria sp900113225	79.216	672	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_001653795.1	s__Mitsuaria sp001653795	79.1423	572	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904426505.1	s__Rubrivivax sp904426505	79.1166	608	1815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:50,195] [INFO] GTDB search result was written to GCF_023721835.1_ASM2372183v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:50,196] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:50,199] [INFO] DFAST_QC result json was written to GCF_023721835.1_ASM2372183v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:50,199] [INFO] DFAST_QC completed!
[2024-01-25 18:42:50,199] [INFO] Total running time: 0h2m29s