[2024-01-24 11:43:50,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:50,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:50,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference
[2024-01-24 11:43:51,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:51,847] [INFO] Task started: Prodigal
[2024-01-24 11:43:51,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d4f4ff1-bd02-4957-80f2-82cc6bd33229/GCF_002933415.1_ASM293341v1_genomic.fna.gz | prodigal -d GCF_002933415.1_ASM293341v1_genomic.fna/cds.fna -a GCF_002933415.1_ASM293341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:03,434] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:03,434] [INFO] Task started: HMMsearch
[2024-01-24 11:44:03,434] [INFO] Running command: hmmsearch --tblout GCF_002933415.1_ASM293341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference/reference_markers.hmm GCF_002933415.1_ASM293341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:03,673] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:03,674] [INFO] Found 6/6 markers.
[2024-01-24 11:44:03,705] [INFO] Query marker FASTA was written to GCF_002933415.1_ASM293341v1_genomic.fna/markers.fasta
[2024-01-24 11:44:03,705] [INFO] Task started: Blastn
[2024-01-24 11:44:03,705] [INFO] Running command: blastn -query GCF_002933415.1_ASM293341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference/reference_markers.fasta -out GCF_002933415.1_ASM293341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:04,766] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:04,769] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:04,769] [INFO] Target genome list was writen to GCF_002933415.1_ASM293341v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:04,774] [INFO] Task started: fastANI
[2024-01-24 11:44:04,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d4f4ff1-bd02-4957-80f2-82cc6bd33229/GCF_002933415.1_ASM293341v1_genomic.fna.gz --refList GCF_002933415.1_ASM293341v1_genomic.fna/target_genomes.txt --output GCF_002933415.1_ASM293341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:19,614] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:19,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:19,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:19,627] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:19,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:19,627] [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	100.0	1250	1251	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	99.9961	1251	1251	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	99.9951	1246	1251	95	conclusive
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	82.1498	821	1251	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.4132	643	1251	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	81.3113	646	1251	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.796	755	1251	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.7802	731	1251	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.7448	720	1251	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.7251	591	1251	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.5535	574	1251	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.5504	651	1251	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	80.433	521	1251	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	80.1762	529	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:19,629] [INFO] DFAST Taxonomy check result was written to GCF_002933415.1_ASM293341v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:19,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:19,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:19,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference/checkm_data
[2024-01-24 11:44:19,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:19,668] [INFO] Task started: CheckM
[2024-01-24 11:44:19,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002933415.1_ASM293341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002933415.1_ASM293341v1_genomic.fna/checkm_input GCF_002933415.1_ASM293341v1_genomic.fna/checkm_result
[2024-01-24 11:45:19,914] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:19,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:19,931] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:19,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:19,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002933415.1_ASM293341v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:19,932] [INFO] Task started: Blastn
[2024-01-24 11:45:19,932] [INFO] Running command: blastn -query GCF_002933415.1_ASM293341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbba3170-e625-4962-a00d-45a2883b927b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002933415.1_ASM293341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:22,144] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:22,147] [INFO] Selected 20 target genomes.
[2024-01-24 11:45:22,148] [INFO] Target genome list was writen to GCF_002933415.1_ASM293341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:22,176] [INFO] Task started: fastANI
[2024-01-24 11:45:22,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d4f4ff1-bd02-4957-80f2-82cc6bd33229/GCF_002933415.1_ASM293341v1_genomic.fna.gz --refList GCF_002933415.1_ASM293341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002933415.1_ASM293341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:43,845] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:43,861] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:43,861] [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	99.9961	1251	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	conclusive
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	82.7521	778	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001017435.1	s__Polyangium_A brachysporum	82.1355	822	1251	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_004011805.1	s__Piscinibacter defluvii	82.0649	806	1251	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	82.0593	800	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930615.1	s__Zhizhongheella caldifontis	81.9993	696	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Zhizhongheella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795745.1	s__Piscinibacter sp017795745	81.7391	743	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	81.6392	784	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	81.6072	765	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	81.4398	760	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219375.1	s__Aquabacterium sp016219375	81.4251	632	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294065.1	s__Sphaerotilus sp013294065	81.3807	686	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	80.9874	706	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_015624425.1	s__Kinneretia sp015624425	80.9147	735	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	80.89	543	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113225.1	s__Mitsuaria sp900113225	80.68	691	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	80.5736	662	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_002761755.1	s__Mitsuaria sp002761755	80.5728	648	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735685.1	s__SJAQ100 sp016735685	80.5049	521	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SJAQ100	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	79.0249	529	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:43,863] [INFO] GTDB search result was written to GCF_002933415.1_ASM293341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:43,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:43,867] [INFO] DFAST_QC result json was written to GCF_002933415.1_ASM293341v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:43,867] [INFO] DFAST_QC completed!
[2024-01-24 11:45:43,867] [INFO] Total running time: 0h1m53s