[2023-06-30 14:53:55,979] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:53:55,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:53:55,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference
[2023-06-30 14:53:57,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:53:57,255] [INFO] Task started: Prodigal
[2023-06-30 14:53:57,255] [INFO] Running command: gunzip -c /var/lib/cwl/stgf174ca19-aefd-4979-96ae-f3b5f7a21cf5/GCA_024708915.1_ASM2470891v1_genomic.fna.gz | prodigal -d GCA_024708915.1_ASM2470891v1_genomic.fna/cds.fna -a GCA_024708915.1_ASM2470891v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:06,466] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:06,466] [INFO] Task started: HMMsearch
[2023-06-30 14:54:06,466] [INFO] Running command: hmmsearch --tblout GCA_024708915.1_ASM2470891v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference/reference_markers.hmm GCA_024708915.1_ASM2470891v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:06,718] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:06,720] [INFO] Found 6/6 markers.
[2023-06-30 14:54:06,755] [INFO] Query marker FASTA was written to GCA_024708915.1_ASM2470891v1_genomic.fna/markers.fasta
[2023-06-30 14:54:06,756] [INFO] Task started: Blastn
[2023-06-30 14:54:06,756] [INFO] Running command: blastn -query GCA_024708915.1_ASM2470891v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference/reference_markers.fasta -out GCA_024708915.1_ASM2470891v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:07,730] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:07,734] [INFO] Selected 23 target genomes.
[2023-06-30 14:54:07,734] [INFO] Target genome list was writen to GCA_024708915.1_ASM2470891v1_genomic.fna/target_genomes.txt
[2023-06-30 14:54:07,736] [INFO] Task started: fastANI
[2023-06-30 14:54:07,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgf174ca19-aefd-4979-96ae-f3b5f7a21cf5/GCA_024708915.1_ASM2470891v1_genomic.fna.gz --refList GCA_024708915.1_ASM2470891v1_genomic.fna/target_genomes.txt --output GCA_024708915.1_ASM2470891v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:23,467] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:23,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:23,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:23,486] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:23,487] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:54:23,487] [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
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	91.9631	725	977	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	84.0492	607	977	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	78.8163	272	977	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	78.7087	283	977	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.5299	238	977	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	78.5208	239	977	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.1731	213	977	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	78.053	235	977	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.8681	255	977	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.8518	193	977	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	77.6013	198	977	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.5732	209	977	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	77.5366	188	977	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	77.5249	186	977	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.5165	285	977	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	77.4686	244	977	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.31	170	977	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	77.2056	181	977	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.1445	147	977	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	77.027	241	977	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	76.7052	86	977	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	76.6922	146	977	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	76.0701	106	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:54:23,490] [INFO] DFAST Taxonomy check result was written to GCA_024708915.1_ASM2470891v1_genomic.fna/tc_result.tsv
[2023-06-30 14:54:23,491] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:23,491] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:23,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference/checkm_data
[2023-06-30 14:54:23,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:23,535] [INFO] Task started: CheckM
[2023-06-30 14:54:23,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708915.1_ASM2470891v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708915.1_ASM2470891v1_genomic.fna/checkm_input GCA_024708915.1_ASM2470891v1_genomic.fna/checkm_result
[2023-06-30 14:54:55,007] [INFO] Task succeeded: CheckM
[2023-06-30 14:54:55,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 12.50%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 14:54:55,034] [INFO] ===== Completeness check finished =====
[2023-06-30 14:54:55,034] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:54:55,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708915.1_ASM2470891v1_genomic.fna/markers.fasta)
[2023-06-30 14:54:55,035] [INFO] Task started: Blastn
[2023-06-30 14:54:55,035] [INFO] Running command: blastn -query GCA_024708915.1_ASM2470891v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0db9254a-4108-4ea5-9da3-cc882045cb41/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708915.1_ASM2470891v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:56,891] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:56,896] [INFO] Selected 14 target genomes.
[2023-06-30 14:54:56,896] [INFO] Target genome list was writen to GCA_024708915.1_ASM2470891v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:54:56,921] [INFO] Task started: fastANI
[2023-06-30 14:54:56,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgf174ca19-aefd-4979-96ae-f3b5f7a21cf5/GCA_024708915.1_ASM2470891v1_genomic.fna.gz --refList GCA_024708915.1_ASM2470891v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708915.1_ASM2470891v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:55:06,818] [INFO] Task succeeded: fastANI
[2023-06-30 14:55:06,835] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:55:06,835] [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_001897675.1	s__Thiobacillus sp001897675	92.1203	650	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	95.41	95.18	0.77	0.76	3	-
GCF_000376425.1	s__Thiobacillus denitrificans	91.9631	725	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820765.1	s__Thiobacillus sp018820765	85.6417	621	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_002256995.1	s__Thiobacillus sp002256995	85.284	586	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.94	97.93	0.93	0.88	3	-
GCA_003510325.1	s__Thiobacillus sp003510325	85.2334	472	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.33	99.33	0.73	0.73	2	-
GCA_018262815.1	s__Thiobacillus sp018262815	85.1917	508	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001530125.1	s__Thiobacillus denitrificans_C	85.1844	606	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	84.9219	551	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016195805.1	s__Thiobacillus sp016195805	84.8888	597	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899765.1	s__Thiobacillus sp001899765	84.5234	639	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.02	98.01	0.93	0.89	5	-
GCA_001899305.1	s__Thiobacillus sp001899305	84.2093	618	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.65	95.89	0.93	0.87	5	-
GCA_002343685.1	s__Thiobacillus denitrificans_A	84.1503	561	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCF_000373385.1	s__Thiobacillus thioparus	84.0561	605	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820745.1	s__Thiobacillus sp018820745	84.0089	367	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:55:06,837] [INFO] GTDB search result was written to GCA_024708915.1_ASM2470891v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:55:06,838] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:55:06,842] [INFO] DFAST_QC result json was written to GCA_024708915.1_ASM2470891v1_genomic.fna/dqc_result.json
[2023-06-30 14:55:06,842] [INFO] DFAST_QC completed!
[2023-06-30 14:55:06,842] [INFO] Total running time: 0h1m11s