[2024-01-25 17:46:50,560] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:50,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:50,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference
[2024-01-25 17:46:51,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:51,656] [INFO] Task started: Prodigal
[2024-01-25 17:46:51,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg5652d565-e478-4ac1-9a02-fab7a19747e0/GCF_016909025.1_ASM1690902v1_genomic.fna.gz | prodigal -d GCF_016909025.1_ASM1690902v1_genomic.fna/cds.fna -a GCF_016909025.1_ASM1690902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:58,964] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:58,964] [INFO] Task started: HMMsearch
[2024-01-25 17:46:58,964] [INFO] Running command: hmmsearch --tblout GCF_016909025.1_ASM1690902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference/reference_markers.hmm GCF_016909025.1_ASM1690902v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:59,188] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:59,189] [INFO] Found 6/6 markers.
[2024-01-25 17:46:59,233] [INFO] Query marker FASTA was written to GCF_016909025.1_ASM1690902v1_genomic.fna/markers.fasta
[2024-01-25 17:46:59,234] [INFO] Task started: Blastn
[2024-01-25 17:46:59,234] [INFO] Running command: blastn -query GCF_016909025.1_ASM1690902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference/reference_markers.fasta -out GCF_016909025.1_ASM1690902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:59,794] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:59,797] [INFO] Selected 10 target genomes.
[2024-01-25 17:46:59,797] [INFO] Target genome list was writen to GCF_016909025.1_ASM1690902v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:59,811] [INFO] Task started: fastANI
[2024-01-25 17:46:59,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg5652d565-e478-4ac1-9a02-fab7a19747e0/GCF_016909025.1_ASM1690902v1_genomic.fna.gz --refList GCF_016909025.1_ASM1690902v1_genomic.fna/target_genomes.txt --output GCF_016909025.1_ASM1690902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:08,084] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:08,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:08,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:08,094] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:47:08,094] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:47:08,094] [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=DSM 101595	GCA_016909025.1	1748298	1748298	type	True	100.0	1257	1258	95	inconclusive
Solibacillus kalamii	strain=ISSFR-015	GCA_002174535.1	1748298	1748298	type	True	99.9956	1255	1258	95	inconclusive
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	97.086	1153	1258	95	inconclusive
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	82.7337	770	1258	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	82.665	790	1258	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	79.2	431	1258	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	78.9338	218	1258	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.2355	204	1258	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.966	189	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:08,096] [INFO] DFAST Taxonomy check result was written to GCF_016909025.1_ASM1690902v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:08,096] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:08,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:08,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference/checkm_data
[2024-01-25 17:47:08,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:08,143] [INFO] Task started: CheckM
[2024-01-25 17:47:08,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909025.1_ASM1690902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909025.1_ASM1690902v1_genomic.fna/checkm_input GCF_016909025.1_ASM1690902v1_genomic.fna/checkm_result
[2024-01-25 17:47:34,696] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:34,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:34,724] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:34,724] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:34,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909025.1_ASM1690902v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:34,725] [INFO] Task started: Blastn
[2024-01-25 17:47:34,725] [INFO] Running command: blastn -query GCF_016909025.1_ASM1690902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ad54d2-c7ef-413a-abf9-471df0fe52bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909025.1_ASM1690902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:35,507] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:35,511] [INFO] Selected 11 target genomes.
[2024-01-25 17:47:35,511] [INFO] Target genome list was writen to GCF_016909025.1_ASM1690902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:35,547] [INFO] Task started: fastANI
[2024-01-25 17:47:35,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg5652d565-e478-4ac1-9a02-fab7a19747e0/GCF_016909025.1_ASM1690902v1_genomic.fna.gz --refList GCF_016909025.1_ASM1690902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909025.1_ASM1690902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:43,967] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:43,975] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:43,975] [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	97.036	1175	1258	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	91.1481	1057	1258	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	82.7358	770	1258	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	82.6575	791	1258	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	80.3614	508	1258	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	79.175	435	1258	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	78.9338	218	1258	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	78.3002	209	1258	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	77.471	131	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:43,976] [INFO] GTDB search result was written to GCF_016909025.1_ASM1690902v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:43,977] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:43,979] [INFO] DFAST_QC result json was written to GCF_016909025.1_ASM1690902v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:43,979] [INFO] DFAST_QC completed!
[2024-01-25 17:47:43,979] [INFO] Total running time: 0h0m53s