[2024-01-24 13:37:05,103] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference
[2024-01-24 13:37:06,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,424] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d867d76-e632-4989-adff-e43b4fd245b6/GCF_013366375.1_ASM1336637v1_genomic.fna.gz | prodigal -d GCF_013366375.1_ASM1336637v1_genomic.fna/cds.fna -a GCF_013366375.1_ASM1336637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:23,562] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:23,562] [INFO] Task started: HMMsearch
[2024-01-24 13:37:23,562] [INFO] Running command: hmmsearch --tblout GCF_013366375.1_ASM1336637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference/reference_markers.hmm GCF_013366375.1_ASM1336637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:23,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:23,991] [INFO] Found 6/6 markers.
[2024-01-24 13:37:24,035] [INFO] Query marker FASTA was written to GCF_013366375.1_ASM1336637v1_genomic.fna/markers.fasta
[2024-01-24 13:37:24,036] [INFO] Task started: Blastn
[2024-01-24 13:37:24,036] [INFO] Running command: blastn -query GCF_013366375.1_ASM1336637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference/reference_markers.fasta -out GCF_013366375.1_ASM1336637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:25,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:25,198] [INFO] Selected 18 target genomes.
[2024-01-24 13:37:25,198] [INFO] Target genome list was writen to GCF_013366375.1_ASM1336637v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:25,204] [INFO] Task started: fastANI
[2024-01-24 13:37:25,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d867d76-e632-4989-adff-e43b4fd245b6/GCF_013366375.1_ASM1336637v1_genomic.fna.gz --refList GCF_013366375.1_ASM1336637v1_genomic.fna/target_genomes.txt --output GCF_013366375.1_ASM1336637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:45,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:45,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:45,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:45,276] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:45,276] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:45,276] [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_003349825.1	215580	215580	type	True	79.9591	637	1837	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.9376	635	1837	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.9375	650	1837	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.9197	631	1837	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	79.8962	665	1837	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.4689	699	1837	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.4391	703	1837	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.2669	578	1837	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.0745	553	1837	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.0699	554	1837	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	78.6224	573	1837	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.621	659	1837	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.6082	651	1837	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.5786	577	1837	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	78.5748	625	1837	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	78.4903	534	1837	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.3834	545	1837	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.1199	552	1837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:45,278] [INFO] DFAST Taxonomy check result was written to GCF_013366375.1_ASM1336637v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:45,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:45,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:45,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference/checkm_data
[2024-01-24 13:37:45,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:45,332] [INFO] Task started: CheckM
[2024-01-24 13:37:45,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013366375.1_ASM1336637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013366375.1_ASM1336637v1_genomic.fna/checkm_input GCF_013366375.1_ASM1336637v1_genomic.fna/checkm_result
[2024-01-24 13:38:55,592] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:55,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:55,616] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:55,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:55,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013366375.1_ASM1336637v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:55,617] [INFO] Task started: Blastn
[2024-01-24 13:38:55,618] [INFO] Running command: blastn -query GCF_013366375.1_ASM1336637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b9101c-6647-4390-ba39-ce7070d816c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_013366375.1_ASM1336637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:57,900] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:57,903] [INFO] Selected 19 target genomes.
[2024-01-24 13:38:57,904] [INFO] Target genome list was writen to GCF_013366375.1_ASM1336637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:57,948] [INFO] Task started: fastANI
[2024-01-24 13:38:57,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d867d76-e632-4989-adff-e43b4fd245b6/GCF_013366375.1_ASM1336637v1_genomic.fna.gz --refList GCF_013366375.1_ASM1336637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013366375.1_ASM1336637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:21,642] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:21,663] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:21,664] [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_013366375.1	s__Schlegelella_A koreensis	100.0	1834	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017881025.1	s__Schlegelella_A sp017881025	82.0119	693	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425865.1	s__LMDS01 sp001425865	81.2546	794	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241265.1	s__JAFEEF01 sp018241265	80.885	776	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFEEF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	80.7958	892	1837	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	80.6666	827	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	80.6444	821	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799605.1	s__Rhizobacter sp000799605	80.5273	807	1837	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	80.5193	805	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293525.1	s__Ideonella_A sakaiensis	80.4702	824	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	80.4624	806	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795745.1	s__Piscinibacter sp017795745	80.449	728	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425825.1	s__Rhizobacter sp001425825	80.4302	809	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
GCA_016702655.1	s__CAIKUF01 sp016702655	80.1642	687	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826655.1	s__Methylibium sp902826655	80.1613	632	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001263235.1	s__LMDS01 sp001263235	80.0115	660	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	79.9595	647	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	79.6707	722	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCF_016467315.1	s__OAE585 sp016467315	78.9654	732	1837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:21,666] [INFO] GTDB search result was written to GCF_013366375.1_ASM1336637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:21,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:21,674] [INFO] DFAST_QC result json was written to GCF_013366375.1_ASM1336637v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:21,675] [INFO] DFAST_QC completed!
[2024-01-24 13:39:21,675] [INFO] Total running time: 0h2m17s