[2024-01-24 14:30:46,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:46,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:46,404] [INFO] DQC Reference Directory: /var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference
[2024-01-24 14:30:47,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:47,674] [INFO] Task started: Prodigal
[2024-01-24 14:30:47,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg59778feb-d42f-4294-84ce-029c555918db/GCF_000828895.1_ASM82889v1_genomic.fna.gz | prodigal -d GCF_000828895.1_ASM82889v1_genomic.fna/cds.fna -a GCF_000828895.1_ASM82889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:56,948] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:56,949] [INFO] Task started: HMMsearch
[2024-01-24 14:30:56,949] [INFO] Running command: hmmsearch --tblout GCF_000828895.1_ASM82889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference/reference_markers.hmm GCF_000828895.1_ASM82889v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:57,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:57,212] [INFO] Found 6/6 markers.
[2024-01-24 14:30:57,239] [INFO] Query marker FASTA was written to GCF_000828895.1_ASM82889v1_genomic.fna/markers.fasta
[2024-01-24 14:30:57,239] [INFO] Task started: Blastn
[2024-01-24 14:30:57,240] [INFO] Running command: blastn -query GCF_000828895.1_ASM82889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference/reference_markers.fasta -out GCF_000828895.1_ASM82889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:58,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:58,076] [INFO] Selected 17 target genomes.
[2024-01-24 14:30:58,076] [INFO] Target genome list was writen to GCF_000828895.1_ASM82889v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:58,086] [INFO] Task started: fastANI
[2024-01-24 14:30:58,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg59778feb-d42f-4294-84ce-029c555918db/GCF_000828895.1_ASM82889v1_genomic.fna.gz --refList GCF_000828895.1_ASM82889v1_genomic.fna/target_genomes.txt --output GCF_000828895.1_ASM82889v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:11,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:11,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:11,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:11,345] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:11,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:11,346] [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
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	100.0	858	858	95	conclusive
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	93.3175	700	858	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	88.2124	678	858	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	79.9664	409	858	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	79.897	418	858	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	79.7447	426	858	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.6927	441	858	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.3142	426	858	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	79.2871	398	858	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	79.2253	376	858	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.2203	345	858	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	79.1784	400	858	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	79.0942	414	858	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.4034	363	858	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	78.2237	306	858	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.1045	340	858	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.7628	307	858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:11,348] [INFO] DFAST Taxonomy check result was written to GCF_000828895.1_ASM82889v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:11,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:11,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:11,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference/checkm_data
[2024-01-24 14:31:11,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:11,388] [INFO] Task started: CheckM
[2024-01-24 14:31:11,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000828895.1_ASM82889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000828895.1_ASM82889v1_genomic.fna/checkm_input GCF_000828895.1_ASM82889v1_genomic.fna/checkm_result
[2024-01-24 14:31:47,555] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:47,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:47,574] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:47,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:47,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000828895.1_ASM82889v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:47,575] [INFO] Task started: Blastn
[2024-01-24 14:31:47,576] [INFO] Running command: blastn -query GCF_000828895.1_ASM82889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfea3b6f7-037d-436a-961f-c1bc64166319/dqc_reference/reference_markers_gtdb.fasta -out GCF_000828895.1_ASM82889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:49,038] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:49,042] [INFO] Selected 14 target genomes.
[2024-01-24 14:31:49,042] [INFO] Target genome list was writen to GCF_000828895.1_ASM82889v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:49,053] [INFO] Task started: fastANI
[2024-01-24 14:31:49,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg59778feb-d42f-4294-84ce-029c555918db/GCF_000828895.1_ASM82889v1_genomic.fna.gz --refList GCF_000828895.1_ASM82889v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000828895.1_ASM82889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:58,751] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:58,765] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:58,765] [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_000828895.1	s__Serpentinomonas raichei	100.0	858	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000696225.1	s__Serpentinomonas sp000696225	93.3344	699	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828915.1	s__Serpentinomonas mccroryi	88.2516	679	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	98.21	97.99	0.96	0.95	3	-
GCF_002837145.1	s__BK-30 sp002837145	80.7008	444	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	79.8949	442	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	79.8846	419	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291945.1	s__UBA997 sp002291945	79.816	384	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA997	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837135.1	s__Macromonas bipunctata	79.5392	382	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	79.2857	398	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980595.1	s__Malikia granosa	79.2748	399	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556675.1	s__Tepidimonas taiwanensis	79.2533	397	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCA_013693755.1	s__Tibeticola sp013693755	79.1834	381	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_013376875.1	s__Acidovorax sp001411535	78.0338	314	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.38	95.78	0.89	0.84	16	-
GCA_016191995.1	s__Rubrivivax sp016191995	77.5911	305	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,767] [INFO] GTDB search result was written to GCF_000828895.1_ASM82889v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:58,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:58,772] [INFO] DFAST_QC result json was written to GCF_000828895.1_ASM82889v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:58,772] [INFO] DFAST_QC completed!
[2024-01-24 14:31:58,772] [INFO] Total running time: 0h1m12s