[2024-01-24 15:26:38,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:38,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:38,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference
[2024-01-24 15:26:40,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,131] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,131] [INFO] Running command: gunzip -c /var/lib/cwl/stgd23c9b23-5aae-4ff2-a56a-9d492fef6022/GCF_030813435.1_ASM3081343v1_genomic.fna.gz | prodigal -d GCF_030813435.1_ASM3081343v1_genomic.fna/cds.fna -a GCF_030813435.1_ASM3081343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:51,351] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:51,351] [INFO] Task started: HMMsearch
[2024-01-24 15:26:51,351] [INFO] Running command: hmmsearch --tblout GCF_030813435.1_ASM3081343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference/reference_markers.hmm GCF_030813435.1_ASM3081343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:51,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:51,708] [INFO] Found 6/6 markers.
[2024-01-24 15:26:51,755] [INFO] Query marker FASTA was written to GCF_030813435.1_ASM3081343v1_genomic.fna/markers.fasta
[2024-01-24 15:26:51,755] [INFO] Task started: Blastn
[2024-01-24 15:26:51,755] [INFO] Running command: blastn -query GCF_030813435.1_ASM3081343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference/reference_markers.fasta -out GCF_030813435.1_ASM3081343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:52,408] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:52,412] [INFO] Selected 28 target genomes.
[2024-01-24 15:26:52,413] [INFO] Target genome list was writen to GCF_030813435.1_ASM3081343v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:52,431] [INFO] Task started: fastANI
[2024-01-24 15:26:52,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgd23c9b23-5aae-4ff2-a56a-9d492fef6022/GCF_030813435.1_ASM3081343v1_genomic.fna.gz --refList GCF_030813435.1_ASM3081343v1_genomic.fna/target_genomes.txt --output GCF_030813435.1_ASM3081343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:11,663] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:11,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:11,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:11,678] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:11,678] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:11,678] [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
Evansella cellulosilytica	strain=DSM 2522	GCA_000177235.2	1413	1413	type	True	77.9511	248	1865	95	below_threshold
Evansella caseinilytica	strain=SP	GCA_900107275.1	1503961	1503961	type	True	77.6534	140	1865	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	77.6475	82	1865	95	below_threshold
Evansella tamaricis	strain=CGMCC 1.15917	GCA_019042215.1	2069301	2069301	type	True	77.6301	234	1865	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.6028	61	1865	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	77.3763	71	1865	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	77.348	102	1865	95	below_threshold
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	77.3224	148	1865	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	77.3052	176	1865	95	below_threshold
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	77.1956	84	1865	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.7991	81	1865	95	below_threshold
Alteribacter populi	strain=FJAT-45347	GCA_002352765.2	2011011	2011011	type	True	76.7829	114	1865	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.6588	112	1865	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.5191	63	1865	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.3598	76	1865	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.2232	56	1865	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.1757	71	1865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:11,680] [INFO] DFAST Taxonomy check result was written to GCF_030813435.1_ASM3081343v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:11,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:11,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:11,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference/checkm_data
[2024-01-24 15:27:11,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:11,737] [INFO] Task started: CheckM
[2024-01-24 15:27:11,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813435.1_ASM3081343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813435.1_ASM3081343v1_genomic.fna/checkm_input GCF_030813435.1_ASM3081343v1_genomic.fna/checkm_result
[2024-01-24 15:27:50,156] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:50,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:50,179] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:50,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:50,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813435.1_ASM3081343v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:50,180] [INFO] Task started: Blastn
[2024-01-24 15:27:50,180] [INFO] Running command: blastn -query GCF_030813435.1_ASM3081343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d36579-8178-4401-9198-6d3c977226f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813435.1_ASM3081343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:50,949] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:50,953] [INFO] Selected 34 target genomes.
[2024-01-24 15:27:50,954] [INFO] Target genome list was writen to GCF_030813435.1_ASM3081343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:50,981] [INFO] Task started: fastANI
[2024-01-24 15:27:50,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgd23c9b23-5aae-4ff2-a56a-9d492fef6022/GCF_030813435.1_ASM3081343v1_genomic.fna.gz --refList GCF_030813435.1_ASM3081343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813435.1_ASM3081343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:15,236] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:15,261] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:28:15,261] [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_004799755.1	s__Fredinandcohnia timonensis_A	78.2571	53	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153425.1	s__Evansella alkalicola	77.9439	213	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000177235.2	s__Evansella cellulosilytica	77.9373	249	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	77.7417	62	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900107275.1	s__Evansella caseinilytica	77.6604	141	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866005.1	s__Anaerobacillus alkalilacustris	77.6475	82	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019042215.1	s__Evansella tamaricis	77.6062	234	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429705.1	s__Alteribacter aurantiacus	77.359	70	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	77.348	102	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	97.46	97.46	0.83	0.83	2	-
GCF_003226325.1	s__Salipaludibacillus keqinensis	77.2777	106	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019695.1	s__Evansella clarkii	77.2726	149	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	-
GCF_001866055.1	s__Anaerobacillus alkalidiazotrophicus	77.1517	85	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111295.1	s__Salipaludibacillus aurantiacus	77.1258	96	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	77.1182	66	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002335805.1	s__FJAT-45350 sp002335805	76.8885	83	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865995.1	s__Anaerobacillus arseniciselenatis	76.7991	81	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	76.6352	111	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008364785.1	s__Bacillus_BS sp008364785	76.5464	52	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	76.5183	63	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	76.2315	71	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_016908495.1	s__Bacillus_BW pakistanensis	76.2209	56	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BW	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120055.1	s__Anaerobacillus sp007120055	76.2028	69	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908835.1	s__Bacillus_AD endoradicis	76.1258	53	1865	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:15,270] [INFO] GTDB search result was written to GCF_030813435.1_ASM3081343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:15,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:15,278] [INFO] DFAST_QC result json was written to GCF_030813435.1_ASM3081343v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:15,279] [INFO] DFAST_QC completed!
[2024-01-24 15:28:15,279] [INFO] Total running time: 0h1m36s