[2023-07-01 02:12:49,852] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:12:49,855] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:12:49,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference
[2023-07-01 02:12:51,154] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:12:51,155] [INFO] Task started: Prodigal
[2023-07-01 02:12:51,155] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e82ddf2-9549-4357-a33a-85e7a11e45b0/GCA_024708885.1_ASM2470888v1_genomic.fna.gz | prodigal -d GCA_024708885.1_ASM2470888v1_genomic.fna/cds.fna -a GCA_024708885.1_ASM2470888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:12:58,865] [INFO] Task succeeded: Prodigal
[2023-07-01 02:12:58,866] [INFO] Task started: HMMsearch
[2023-07-01 02:12:58,866] [INFO] Running command: hmmsearch --tblout GCA_024708885.1_ASM2470888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference/reference_markers.hmm GCA_024708885.1_ASM2470888v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:12:59,106] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:12:59,108] [INFO] Found 6/6 markers.
[2023-07-01 02:12:59,134] [INFO] Query marker FASTA was written to GCA_024708885.1_ASM2470888v1_genomic.fna/markers.fasta
[2023-07-01 02:12:59,134] [INFO] Task started: Blastn
[2023-07-01 02:12:59,135] [INFO] Running command: blastn -query GCA_024708885.1_ASM2470888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference/reference_markers.fasta -out GCA_024708885.1_ASM2470888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:00,085] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:00,111] [INFO] Selected 19 target genomes.
[2023-07-01 02:13:00,111] [INFO] Target genome list was writen to GCA_024708885.1_ASM2470888v1_genomic.fna/target_genomes.txt
[2023-07-01 02:13:00,113] [INFO] Task started: fastANI
[2023-07-01 02:13:00,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e82ddf2-9549-4357-a33a-85e7a11e45b0/GCA_024708885.1_ASM2470888v1_genomic.fna.gz --refList GCA_024708885.1_ASM2470888v1_genomic.fna/target_genomes.txt --output GCA_024708885.1_ASM2470888v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:13:12,970] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:12,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:13:12,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:13:12,990] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:13:12,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:13:12,990] [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	82.6609	495	818	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	81.7642	458	818	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.1134	209	818	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.1025	212	818	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.0413	258	818	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.0187	248	818	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.9793	157	818	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.9188	150	818	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.6092	191	818	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.5826	215	818	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.5625	170	818	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	77.3003	232	818	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	77.2012	220	818	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	77.1984	205	818	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	77.1842	206	818	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.1141	163	818	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.0757	121	818	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	76.6311	98	818	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	76.2819	115	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:13:12,992] [INFO] DFAST Taxonomy check result was written to GCA_024708885.1_ASM2470888v1_genomic.fna/tc_result.tsv
[2023-07-01 02:13:12,993] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:13:12,993] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:13:12,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference/checkm_data
[2023-07-01 02:13:12,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:13:13,026] [INFO] Task started: CheckM
[2023-07-01 02:13:13,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708885.1_ASM2470888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708885.1_ASM2470888v1_genomic.fna/checkm_input GCA_024708885.1_ASM2470888v1_genomic.fna/checkm_result
[2023-07-01 02:13:44,093] [INFO] Task succeeded: CheckM
[2023-07-01 02:13:44,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 02:13:44,119] [INFO] ===== Completeness check finished =====
[2023-07-01 02:13:44,120] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:13:44,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708885.1_ASM2470888v1_genomic.fna/markers.fasta)
[2023-07-01 02:13:44,121] [INFO] Task started: Blastn
[2023-07-01 02:13:44,121] [INFO] Running command: blastn -query GCA_024708885.1_ASM2470888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bcc19b6-c323-47b9-ad03-2493d69a4929/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708885.1_ASM2470888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:45,826] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:45,830] [INFO] Selected 14 target genomes.
[2023-07-01 02:13:45,830] [INFO] Target genome list was writen to GCA_024708885.1_ASM2470888v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:13:45,834] [INFO] Task started: fastANI
[2023-07-01 02:13:45,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e82ddf2-9549-4357-a33a-85e7a11e45b0/GCA_024708885.1_ASM2470888v1_genomic.fna.gz --refList GCA_024708885.1_ASM2470888v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708885.1_ASM2470888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:13:54,654] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:54,680] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 02:13:54,681] [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_001899775.1	s__Thiobacillus sp001899775	88.6112	636	818	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	83.6797	505	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_001897675.1	s__Thiobacillus sp001897675	83.2976	483	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	95.41	95.18	0.77	0.76	3	-
GCA_018820765.1	s__Thiobacillus sp018820765	83.1688	511	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCF_000376425.1	s__Thiobacillus denitrificans	82.6924	493	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195805.1	s__Thiobacillus sp016195805	82.6818	451	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262815.1	s__Thiobacillus sp018262815	82.5102	415	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256995.1	s__Thiobacillus sp002256995	82.3663	495	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.94	97.93	0.93	0.88	3	-
GCA_001899765.1	s__Thiobacillus sp001899765	82.2207	482	818	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	81.9211	473	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.65	95.89	0.93	0.87	5	-
GCF_000373385.1	s__Thiobacillus thioparus	81.7383	460	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343685.1	s__Thiobacillus denitrificans_A	81.6608	425	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCF_000012745.1	s__Thiobacillus denitrificans_B	81.442	476	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008923315.1	s__Thiobacillus sp001897705	81.2957	478	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.92	98.92	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2023-07-01 02:13:54,683] [INFO] GTDB search result was written to GCA_024708885.1_ASM2470888v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:13:54,683] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:13:54,710] [INFO] DFAST_QC result json was written to GCA_024708885.1_ASM2470888v1_genomic.fna/dqc_result.json
[2023-07-01 02:13:54,711] [INFO] DFAST_QC completed!
[2023-07-01 02:13:54,711] [INFO] Total running time: 0h1m5s