[2024-01-24 15:02:36,398] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference
[2024-01-24 15:02:38,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,280] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg04bfe161-72c0-4060-bb19-26e788387d4a/GCF_002174535.1_ASM217453v1_genomic.fna.gz | prodigal -d GCF_002174535.1_ASM217453v1_genomic.fna/cds.fna -a GCF_002174535.1_ASM217453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:46,890] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:46,891] [INFO] Task started: HMMsearch
[2024-01-24 15:02:46,891] [INFO] Running command: hmmsearch --tblout GCF_002174535.1_ASM217453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference/reference_markers.hmm GCF_002174535.1_ASM217453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:47,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:47,289] [INFO] Found 6/6 markers.
[2024-01-24 15:02:47,352] [INFO] Query marker FASTA was written to GCF_002174535.1_ASM217453v1_genomic.fna/markers.fasta
[2024-01-24 15:02:47,352] [INFO] Task started: Blastn
[2024-01-24 15:02:47,353] [INFO] Running command: blastn -query GCF_002174535.1_ASM217453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference/reference_markers.fasta -out GCF_002174535.1_ASM217453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:48,024] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:48,030] [INFO] Selected 10 target genomes.
[2024-01-24 15:02:48,031] [INFO] Target genome list was writen to GCF_002174535.1_ASM217453v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:48,037] [INFO] Task started: fastANI
[2024-01-24 15:02:48,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg04bfe161-72c0-4060-bb19-26e788387d4a/GCF_002174535.1_ASM217453v1_genomic.fna.gz --refList GCF_002174535.1_ASM217453v1_genomic.fna/target_genomes.txt --output GCF_002174535.1_ASM217453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:56,812] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:56,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:56,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:56,829] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:02:56,829] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:02:56,829] [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
Solibacillus kalamii	strain=ISSFR-015	GCA_002174535.1	1748298	1748298	type	True	100.0	1255	1256	95	inconclusive
Solibacillus kalamii	strain=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	99.9986	1247	1256	95	inconclusive
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	97.1309	1144	1256	95	inconclusive
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	82.7467	774	1256	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	82.6258	784	1256	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	79.1956	427	1256	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	78.7765	226	1256	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	78.047	190	1256	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.0189	214	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:56,831] [INFO] DFAST Taxonomy check result was written to GCF_002174535.1_ASM217453v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:56,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:56,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:56,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference/checkm_data
[2024-01-24 15:02:56,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:56,876] [INFO] Task started: CheckM
[2024-01-24 15:02:56,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002174535.1_ASM217453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002174535.1_ASM217453v1_genomic.fna/checkm_input GCF_002174535.1_ASM217453v1_genomic.fna/checkm_result
[2024-01-24 15:03:30,156] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:30,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:30,178] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:30,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:30,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002174535.1_ASM217453v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:30,179] [INFO] Task started: Blastn
[2024-01-24 15:03:30,179] [INFO] Running command: blastn -query GCF_002174535.1_ASM217453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89124953-b42c-4089-a27b-136527e74998/dqc_reference/reference_markers_gtdb.fasta -out GCF_002174535.1_ASM217453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:31,023] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:31,029] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:31,030] [INFO] Target genome list was writen to GCF_002174535.1_ASM217453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:31,042] [INFO] Task started: fastANI
[2024-01-24 15:03:31,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg04bfe161-72c0-4060-bb19-26e788387d4a/GCF_002174535.1_ASM217453v1_genomic.fna.gz --refList GCF_002174535.1_ASM217453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002174535.1_ASM217453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:39,737] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:39,746] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:39,746] [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_001586195.1	s__Solibacillus silvestris	97.1077	1162	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	98.10	97.06	0.93	0.90	6	conclusive
GCF_900168685.1	s__Solibacillus isronensis_A	91.089	1068	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836905.1	s__Solibacillus sp014836905	82.7544	773	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836935.1	s__Solibacillus sp014836935	82.6258	784	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073375.1	s__Solibacillus sp003073375	80.139	531	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001439635.1	s__Solibacillus cecembensis	79.2007	426	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700315.1	s__Caryophanon tenue	78.7774	227	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Caryophanon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000392615.1	s__Lysinibacillus sphaericus_B	78.1531	209	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065935.1	s__Kurthia sp018065935	77.4946	133	1256	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:39,748] [INFO] GTDB search result was written to GCF_002174535.1_ASM217453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:39,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:39,752] [INFO] DFAST_QC result json was written to GCF_002174535.1_ASM217453v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:39,752] [INFO] DFAST_QC completed!
[2024-01-24 15:03:39,752] [INFO] Total running time: 0h1m3s