[2023-06-18 18:31:16,887] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:16,891] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:16,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference
[2023-06-18 18:31:18,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:18,255] [INFO] Task started: Prodigal
[2023-06-18 18:31:18,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg30d928bc-7d51-4400-bf8c-d479557fbcbb/GCA_018820445.1_ASM1882044v1_genomic.fna.gz | prodigal -d GCA_018820445.1_ASM1882044v1_genomic.fna/cds.fna -a GCA_018820445.1_ASM1882044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:31,186] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:31,187] [INFO] Task started: HMMsearch
[2023-06-18 18:31:31,187] [INFO] Running command: hmmsearch --tblout GCA_018820445.1_ASM1882044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference/reference_markers.hmm GCA_018820445.1_ASM1882044v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:31,466] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:31,468] [INFO] Found 6/6 markers.
[2023-06-18 18:31:31,515] [INFO] Query marker FASTA was written to GCA_018820445.1_ASM1882044v1_genomic.fna/markers.fasta
[2023-06-18 18:31:31,516] [INFO] Task started: Blastn
[2023-06-18 18:31:31,516] [INFO] Running command: blastn -query GCA_018820445.1_ASM1882044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference/reference_markers.fasta -out GCA_018820445.1_ASM1882044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:32,356] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:32,364] [INFO] Selected 19 target genomes.
[2023-06-18 18:31:32,365] [INFO] Target genome list was writen to GCA_018820445.1_ASM1882044v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:32,369] [INFO] Task started: fastANI
[2023-06-18 18:31:32,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d928bc-7d51-4400-bf8c-d479557fbcbb/GCA_018820445.1_ASM1882044v1_genomic.fna.gz --refList GCA_018820445.1_ASM1882044v1_genomic.fna/target_genomes.txt --output GCA_018820445.1_ASM1882044v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:46,907] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:46,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:46,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:46,922] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:31:46,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:31:46,923] [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
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	83.0433	794	1399	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	82.9832	792	1399	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	81.9077	674	1399	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	81.8756	641	1399	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.2163	392	1399	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.2044	338	1399	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.9558	300	1399	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.9303	306	1399	95	below_threshold
Fluviibacter phosphoraccumulans	strain=SHINM1	GCA_016110345.1	1751046	1751046	type	True	77.2944	86	1399	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.8861	191	1399	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	76.731	175	1399	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.3272	169	1399	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.311	181	1399	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	76.232	142	1399	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.2273	188	1399	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	75.7778	86	1399	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_019684215.1	1138189	1138189	type	True	75.3071	59	1399	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	75.2803	61	1399	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:31:46,924] [INFO] DFAST Taxonomy check result was written to GCA_018820445.1_ASM1882044v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:46,926] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:46,926] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:46,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference/checkm_data
[2023-06-18 18:31:46,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:46,982] [INFO] Task started: CheckM
[2023-06-18 18:31:46,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018820445.1_ASM1882044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018820445.1_ASM1882044v1_genomic.fna/checkm_input GCA_018820445.1_ASM1882044v1_genomic.fna/checkm_result
[2023-06-18 18:32:26,821] [INFO] Task succeeded: CheckM
[2023-06-18 18:32:26,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:32:26,850] [INFO] ===== Completeness check finished =====
[2023-06-18 18:32:26,850] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:32:26,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018820445.1_ASM1882044v1_genomic.fna/markers.fasta)
[2023-06-18 18:32:26,851] [INFO] Task started: Blastn
[2023-06-18 18:32:26,851] [INFO] Running command: blastn -query GCA_018820445.1_ASM1882044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc52ed029-afaf-41fa-892a-d4263779ce1f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018820445.1_ASM1882044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:32:28,206] [INFO] Task succeeded: Blastn
[2023-06-18 18:32:28,210] [INFO] Selected 14 target genomes.
[2023-06-18 18:32:28,211] [INFO] Target genome list was writen to GCA_018820445.1_ASM1882044v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:32:28,220] [INFO] Task started: fastANI
[2023-06-18 18:32:28,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d928bc-7d51-4400-bf8c-d479557fbcbb/GCA_018820445.1_ASM1882044v1_genomic.fna.gz --refList GCA_018820445.1_ASM1882044v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018820445.1_ASM1882044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:32:39,948] [INFO] Task succeeded: fastANI
[2023-06-18 18:32:39,963] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:32:39,964] [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_018828385.1	s__Azonexus sp018828385	99.9999	1395	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCA_002840785.1	s__Azonexus sp002840785	94.1276	1014	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842145.1	s__Azonexus sp002842145	90.8766	1000	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008080565.1	s__Azonexus sp008080565	88.5204	1011	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780195.1	s__Azonexus sp018780195	88.3285	793	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013335535.1	s__Azonexus sp013335535	86.9195	955	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705475.1	s__Azonexus sp016705475	86.0638	795	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.40	98.37	0.84	0.83	3	-
GCA_018261895.1	s__Azonexus sp018261895	85.1763	751	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922075.1	s__Azonexus sp903922075	83.6509	598	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440665.1	s__Azonexus sp002440665	82.8749	666	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	76.8736	192	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCA_005884255.1	s__VBDL01 sp005884255	76.1884	102	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379915.1	s__JACMKV01 sp014379915	75.7241	55	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JACMKV01;g__JACMKV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:32:39,966] [INFO] GTDB search result was written to GCA_018820445.1_ASM1882044v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:32:39,966] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:32:39,970] [INFO] DFAST_QC result json was written to GCA_018820445.1_ASM1882044v1_genomic.fna/dqc_result.json
[2023-06-18 18:32:39,970] [INFO] DFAST_QC completed!
[2023-06-18 18:32:39,970] [INFO] Total running time: 0h1m23s