[2023-06-13 11:50:38,097] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:50:38,101] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:50:38,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference
[2023-06-13 11:50:39,356] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:50:39,357] [INFO] Task started: Prodigal
[2023-06-13 11:50:39,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg13cd7863-0156-4a2b-b9cb-ccd2264b15a0/GCA_022842425.1_ASM2284242v1_genomic.fna.gz | prodigal -d GCA_022842425.1_ASM2284242v1_genomic.fna/cds.fna -a GCA_022842425.1_ASM2284242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:50:50,448] [INFO] Task succeeded: Prodigal
[2023-06-13 11:50:50,449] [INFO] Task started: HMMsearch
[2023-06-13 11:50:50,449] [INFO] Running command: hmmsearch --tblout GCA_022842425.1_ASM2284242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference/reference_markers.hmm GCA_022842425.1_ASM2284242v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:50:50,758] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:50:50,760] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13cd7863-0156-4a2b-b9cb-ccd2264b15a0/GCA_022842425.1_ASM2284242v1_genomic.fna.gz]
[2023-06-13 11:50:50,799] [INFO] Query marker FASTA was written to GCA_022842425.1_ASM2284242v1_genomic.fna/markers.fasta
[2023-06-13 11:50:50,800] [INFO] Task started: Blastn
[2023-06-13 11:50:50,800] [INFO] Running command: blastn -query GCA_022842425.1_ASM2284242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference/reference_markers.fasta -out GCA_022842425.1_ASM2284242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:51,644] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:51,648] [INFO] Selected 23 target genomes.
[2023-06-13 11:50:51,649] [INFO] Target genome list was writen to GCA_022842425.1_ASM2284242v1_genomic.fna/target_genomes.txt
[2023-06-13 11:50:51,652] [INFO] Task started: fastANI
[2023-06-13 11:50:51,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg13cd7863-0156-4a2b-b9cb-ccd2264b15a0/GCA_022842425.1_ASM2284242v1_genomic.fna.gz --refList GCA_022842425.1_ASM2284242v1_genomic.fna/target_genomes.txt --output GCA_022842425.1_ASM2284242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:51:06,300] [INFO] Task succeeded: fastANI
[2023-06-13 11:51:06,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:51:06,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:51:06,319] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:51:06,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:51:06,320] [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
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	76.9561	127	1080	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.9164	112	1080	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.9164	112	1080	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.8767	86	1080	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.8394	85	1080	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.8352	136	1080	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	76.7937	107	1080	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	76.7765	101	1080	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.752	109	1080	95	below_threshold
Methyloversatilis thermotolerans	strain=3t	GCA_000372885.1	1346290	1346290	type	True	76.7402	100	1080	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	76.723	127	1080	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.7183	65	1080	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	76.4382	67	1080	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	76.4199	88	1080	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	76.3489	138	1080	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	76.3248	137	1080	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.2039	66	1080	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	76.1644	108	1080	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	76.1571	120	1080	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	76.1161	91	1080	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	76.0645	95	1080	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	75.3836	62	1080	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	75.3415	62	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:51:06,322] [INFO] DFAST Taxonomy check result was written to GCA_022842425.1_ASM2284242v1_genomic.fna/tc_result.tsv
[2023-06-13 11:51:06,323] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:51:06,323] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:51:06,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference/checkm_data
[2023-06-13 11:51:06,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:51:06,376] [INFO] Task started: CheckM
[2023-06-13 11:51:06,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022842425.1_ASM2284242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022842425.1_ASM2284242v1_genomic.fna/checkm_input GCA_022842425.1_ASM2284242v1_genomic.fna/checkm_result
[2023-06-13 11:51:41,447] [INFO] Task succeeded: CheckM
[2023-06-13 11:51:41,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 11:51:41,478] [INFO] ===== Completeness check finished =====
[2023-06-13 11:51:41,478] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:51:41,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022842425.1_ASM2284242v1_genomic.fna/markers.fasta)
[2023-06-13 11:51:41,479] [INFO] Task started: Blastn
[2023-06-13 11:51:41,479] [INFO] Running command: blastn -query GCA_022842425.1_ASM2284242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99dad9e4-e684-4ea3-9790-d3ffe7626f17/dqc_reference/reference_markers_gtdb.fasta -out GCA_022842425.1_ASM2284242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:51:42,809] [INFO] Task succeeded: Blastn
[2023-06-13 11:51:42,813] [INFO] Selected 13 target genomes.
[2023-06-13 11:51:42,813] [INFO] Target genome list was writen to GCA_022842425.1_ASM2284242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:51:42,817] [INFO] Task started: fastANI
[2023-06-13 11:51:42,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg13cd7863-0156-4a2b-b9cb-ccd2264b15a0/GCA_022842425.1_ASM2284242v1_genomic.fna.gz --refList GCA_022842425.1_ASM2284242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022842425.1_ASM2284242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:51:51,803] [INFO] Task succeeded: fastANI
[2023-06-13 11:51:51,816] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:51:51,816] [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
GCA_001464765.1	s__Ga0077526 sp001464765	98.1029	902	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001464895.1	s__Ga0077526 sp001464895	79.6387	348	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713305.1	s__Ga0077526 sp016713305	78.8765	358	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	98.25	98.25	0.92	0.92	2	-
GCA_016125475.1	s__Ga0077526 sp016125475	78.4519	333	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464695.1	s__Ga0077523 sp001464695	78.0311	309	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077523	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821865.1	s__PNJM01 sp013821865	76.8592	95	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__PNJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909415.1	s__CAIVVS01 sp903909415	76.535	111	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAIVVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218025.1	s__Sulfuritalea sp006218025	76.5222	100	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016235805.1	s__Sulfuritalea sp016235805	76.5148	86	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	76.4199	88	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177575.1	s__RBG-16-66-20 sp016177575	76.2621	71	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__RBG-16-66-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899065.1	s__Devosia_A sp001899065	75.2128	54	1080	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.96	98.00	0.93	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-13 11:51:51,818] [INFO] GTDB search result was written to GCA_022842425.1_ASM2284242v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:51:51,819] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:51:51,823] [INFO] DFAST_QC result json was written to GCA_022842425.1_ASM2284242v1_genomic.fna/dqc_result.json
[2023-06-13 11:51:51,823] [INFO] DFAST_QC completed!
[2023-06-13 11:51:51,823] [INFO] Total running time: 0h1m14s