[2024-01-24 13:32:11,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:11,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:11,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference
[2024-01-24 13:32:14,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,742] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d540de8-7c7b-4c1a-898e-7b19f184705f/GCF_002884435.1_ASM288443v1_genomic.fna.gz | prodigal -d GCF_002884435.1_ASM288443v1_genomic.fna/cds.fna -a GCF_002884435.1_ASM288443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:23,801] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:23,802] [INFO] Task started: HMMsearch
[2024-01-24 13:32:23,802] [INFO] Running command: hmmsearch --tblout GCF_002884435.1_ASM288443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference/reference_markers.hmm GCF_002884435.1_ASM288443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:24,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:24,182] [INFO] Found 6/6 markers.
[2024-01-24 13:32:24,223] [INFO] Query marker FASTA was written to GCF_002884435.1_ASM288443v1_genomic.fna/markers.fasta
[2024-01-24 13:32:24,224] [INFO] Task started: Blastn
[2024-01-24 13:32:24,224] [INFO] Running command: blastn -query GCF_002884435.1_ASM288443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference/reference_markers.fasta -out GCF_002884435.1_ASM288443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:24,843] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:24,847] [INFO] Selected 21 target genomes.
[2024-01-24 13:32:24,847] [INFO] Target genome list was writen to GCF_002884435.1_ASM288443v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:24,882] [INFO] Task started: fastANI
[2024-01-24 13:32:24,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d540de8-7c7b-4c1a-898e-7b19f184705f/GCF_002884435.1_ASM288443v1_genomic.fna.gz --refList GCF_002884435.1_ASM288443v1_genomic.fna/target_genomes.txt --output GCF_002884435.1_ASM288443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:38,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:38,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:38,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:38,130] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:38,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:38,131] [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
Terribacillus goriensis	strain=DSM 18252	GCA_002884435.1	386490	386490	type	True	100.0	1205	1206	95	conclusive
Terribacillus halophilus	strain=DSM 21620	GCA_900101385.1	361279	361279	type	True	83.4904	899	1206	95	below_threshold
Terribacillus aidingensis	strain=CGMCC 1.8913	GCA_900215625.1	586416	586416	type	True	80.3183	682	1206	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.9962	55	1206	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.0375	50	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:38,132] [INFO] DFAST Taxonomy check result was written to GCF_002884435.1_ASM288443v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:38,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:38,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:38,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference/checkm_data
[2024-01-24 13:32:38,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:38,174] [INFO] Task started: CheckM
[2024-01-24 13:32:38,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002884435.1_ASM288443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002884435.1_ASM288443v1_genomic.fna/checkm_input GCF_002884435.1_ASM288443v1_genomic.fna/checkm_result
[2024-01-24 13:33:10,709] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:10,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:10,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:10,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002884435.1_ASM288443v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:10,737] [INFO] Task started: Blastn
[2024-01-24 13:33:10,737] [INFO] Running command: blastn -query GCF_002884435.1_ASM288443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153810b3-e43b-44e9-8cc0-39203aa2c066/dqc_reference/reference_markers_gtdb.fasta -out GCF_002884435.1_ASM288443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,555] [INFO] Selected 6 target genomes.
[2024-01-24 13:33:11,555] [INFO] Target genome list was writen to GCF_002884435.1_ASM288443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:11,561] [INFO] Task started: fastANI
[2024-01-24 13:33:11,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d540de8-7c7b-4c1a-898e-7b19f184705f/GCF_002884435.1_ASM288443v1_genomic.fna.gz --refList GCF_002884435.1_ASM288443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002884435.1_ASM288443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:17,622] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:17,639] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:17,639] [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_900110015.1	s__Terribacillus saccharophilus	98.2474	1122	1206	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	98.11	97.97	0.93	0.93	3	conclusive
GCF_002272745.1	s__Terribacillus saccharophilus_B	91.6273	1031	1206	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	99.16	99.09	0.95	0.94	5	-
GCF_002272075.1	s__Terribacillus saccharophilus_A	90.99	1021	1206	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	99.18	98.32	0.96	0.91	5	-
GCF_002272135.1	s__Terribacillus sp002272135	88.4355	1019	1206	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101385.1	s__Terribacillus halophilus	83.4979	898	1206	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002271665.1	s__Terribacillus sp002271665	82.5077	810	1206	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:17,642] [INFO] GTDB search result was written to GCF_002884435.1_ASM288443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:17,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:17,648] [INFO] DFAST_QC result json was written to GCF_002884435.1_ASM288443v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:17,649] [INFO] DFAST_QC completed!
[2024-01-24 13:33:17,649] [INFO] Total running time: 0h1m6s