[2024-01-24 12:36:23,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:23,111] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:23,111] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference
[2024-01-24 12:36:24,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:24,373] [INFO] Task started: Prodigal
[2024-01-24 12:36:24,373] [INFO] Running command: gunzip -c /var/lib/cwl/stga70bf824-7990-4fe2-ad29-5b4812714f70/GCF_015476235.1_ASM1547623v1_genomic.fna.gz | prodigal -d GCF_015476235.1_ASM1547623v1_genomic.fna/cds.fna -a GCF_015476235.1_ASM1547623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:36,235] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:36,236] [INFO] Task started: HMMsearch
[2024-01-24 12:36:36,236] [INFO] Running command: hmmsearch --tblout GCF_015476235.1_ASM1547623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference/reference_markers.hmm GCF_015476235.1_ASM1547623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:36,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:36,510] [INFO] Found 6/6 markers.
[2024-01-24 12:36:36,545] [INFO] Query marker FASTA was written to GCF_015476235.1_ASM1547623v1_genomic.fna/markers.fasta
[2024-01-24 12:36:36,545] [INFO] Task started: Blastn
[2024-01-24 12:36:36,545] [INFO] Running command: blastn -query GCF_015476235.1_ASM1547623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference/reference_markers.fasta -out GCF_015476235.1_ASM1547623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:37,638] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:37,641] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:37,641] [INFO] Target genome list was writen to GCF_015476235.1_ASM1547623v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:37,653] [INFO] Task started: fastANI
[2024-01-24 12:36:37,654] [INFO] Running command: fastANI --query /var/lib/cwl/stga70bf824-7990-4fe2-ad29-5b4812714f70/GCF_015476235.1_ASM1547623v1_genomic.fna.gz --refList GCF_015476235.1_ASM1547623v1_genomic.fna/target_genomes.txt --output GCF_015476235.1_ASM1547623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:52,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:52,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:52,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:52,781] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:36:52,782] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:52,782] [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_015476235.1	215580	215580	type	True	100.0	1285	1286	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	99.9806	1261	1286	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	99.9673	1253	1286	95	conclusive
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	82.1829	824	1286	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	81.4487	652	1286	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	81.2395	663	1286	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.8422	609	1286	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.8322	728	1286	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	80.7833	730	1286	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.6721	586	1286	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.6612	653	1286	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.6112	783	1286	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	80.3622	520	1286	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	80.0819	540	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:52,784] [INFO] DFAST Taxonomy check result was written to GCF_015476235.1_ASM1547623v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:52,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:52,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:52,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference/checkm_data
[2024-01-24 12:36:52,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:52,834] [INFO] Task started: CheckM
[2024-01-24 12:36:52,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015476235.1_ASM1547623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015476235.1_ASM1547623v1_genomic.fna/checkm_input GCF_015476235.1_ASM1547623v1_genomic.fna/checkm_result
[2024-01-24 12:38:19,440] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:19,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:19,462] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:19,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:19,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015476235.1_ASM1547623v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:19,463] [INFO] Task started: Blastn
[2024-01-24 12:38:19,463] [INFO] Running command: blastn -query GCF_015476235.1_ASM1547623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3a47bf-7654-4de9-859a-a6e0ac175cc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_015476235.1_ASM1547623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:21,750] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:21,754] [INFO] Selected 20 target genomes.
[2024-01-24 12:38:21,755] [INFO] Target genome list was writen to GCF_015476235.1_ASM1547623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:21,775] [INFO] Task started: fastANI
[2024-01-24 12:38:21,775] [INFO] Running command: fastANI --query /var/lib/cwl/stga70bf824-7990-4fe2-ad29-5b4812714f70/GCF_015476235.1_ASM1547623v1_genomic.fna.gz --refList GCF_015476235.1_ASM1547623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015476235.1_ASM1547623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:44,929] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:44,946] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:44,946] [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	100.0	1285	1286	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	82.7155	798	1286	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	82.1391	829	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polyangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	82.1086	787	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	82.0079	812	1286	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	81.8891	710	1286	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	81.8155	749	1286	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	81.6937	790	1286	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	81.5767	801	1286	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	81.5158	782	1286	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	81.4637	635	1286	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	81.2808	704	1286	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	81.1088	710	1286	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	80.9926	753	1286	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	80.7942	557	1286	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	80.7132	700	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_002761755.1	s__Mitsuaria sp002761755	80.6864	649	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	80.6623	672	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_016735685.1	s__SJAQ100 sp016735685	80.4721	530	1286	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	79.0252	524	1286	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 12:38:44,948] [INFO] GTDB search result was written to GCF_015476235.1_ASM1547623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:44,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:44,955] [INFO] DFAST_QC result json was written to GCF_015476235.1_ASM1547623v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:44,956] [INFO] DFAST_QC completed!
[2024-01-24 12:38:44,956] [INFO] Total running time: 0h2m22s