[2024-01-24 12:07:18,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:18,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:18,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference
[2024-01-24 12:07:19,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:19,935] [INFO] Task started: Prodigal
[2024-01-24 12:07:19,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg5633ba23-cac6-42b0-96ab-26adf7c46e2d/GCF_002946355.1_ASM294635v1_genomic.fna.gz | prodigal -d GCF_002946355.1_ASM294635v1_genomic.fna/cds.fna -a GCF_002946355.1_ASM294635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:28,997] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:28,998] [INFO] Task started: HMMsearch
[2024-01-24 12:07:28,998] [INFO] Running command: hmmsearch --tblout GCF_002946355.1_ASM294635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference/reference_markers.hmm GCF_002946355.1_ASM294635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:29,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:29,294] [INFO] Found 6/6 markers.
[2024-01-24 12:07:29,330] [INFO] Query marker FASTA was written to GCF_002946355.1_ASM294635v1_genomic.fna/markers.fasta
[2024-01-24 12:07:29,330] [INFO] Task started: Blastn
[2024-01-24 12:07:29,330] [INFO] Running command: blastn -query GCF_002946355.1_ASM294635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference/reference_markers.fasta -out GCF_002946355.1_ASM294635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:29,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:29,920] [INFO] Selected 23 target genomes.
[2024-01-24 12:07:29,921] [INFO] Target genome list was writen to GCF_002946355.1_ASM294635v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:29,929] [INFO] Task started: fastANI
[2024-01-24 12:07:29,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg5633ba23-cac6-42b0-96ab-26adf7c46e2d/GCF_002946355.1_ASM294635v1_genomic.fna.gz --refList GCF_002946355.1_ASM294635v1_genomic.fna/target_genomes.txt --output GCF_002946355.1_ASM294635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:45,196] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:45,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:45,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:45,209] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:45,209] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:45,209] [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
Pradoshia eiseniae	strain=EAG3	GCA_002946355.1	2064768	2064768	type	True	100.0	1247	1250	95	conclusive
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.1297	66	1250	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.1117	51	1250	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	77.0707	53	1250	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.068	68	1250	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.0478	69	1250	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.0033	51	1250	95	below_threshold
Niallia taxi	strain=M5HDSG1-1	GCA_004005475.1	2499688	2499688	type	True	76.9915	61	1250	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	76.9577	50	1250	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	76.8714	52	1250	95	below_threshold
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	76.8512	68	1250	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	76.8457	65	1250	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	76.8112	55	1250	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.5337	66	1250	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.23	62	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:45,210] [INFO] DFAST Taxonomy check result was written to GCF_002946355.1_ASM294635v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:45,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:45,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:45,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference/checkm_data
[2024-01-24 12:07:45,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:45,255] [INFO] Task started: CheckM
[2024-01-24 12:07:45,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002946355.1_ASM294635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002946355.1_ASM294635v1_genomic.fna/checkm_input GCF_002946355.1_ASM294635v1_genomic.fna/checkm_result
[2024-01-24 12:08:17,344] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:17,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:17,369] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:17,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:17,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002946355.1_ASM294635v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:17,370] [INFO] Task started: Blastn
[2024-01-24 12:08:17,371] [INFO] Running command: blastn -query GCF_002946355.1_ASM294635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6c0f2eb-86f9-4c0d-9e8e-d6b162c56f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_002946355.1_ASM294635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:18,123] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:18,128] [INFO] Selected 16 target genomes.
[2024-01-24 12:08:18,128] [INFO] Target genome list was writen to GCF_002946355.1_ASM294635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:18,139] [INFO] Task started: fastANI
[2024-01-24 12:08:18,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg5633ba23-cac6-42b0-96ab-26adf7c46e2d/GCF_002946355.1_ASM294635v1_genomic.fna.gz --refList GCF_002946355.1_ASM294635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002946355.1_ASM294635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:29,917] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:29,933] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:29,934] [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_002946355.1	s__Pradoshia eiseniae	100.0	1247	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_904501845.1	s__Pradoshia sp904501845	86.1323	729	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_001183965.1	s__Pradoshia sp001183965	82.6297	880	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420715.1	s__Margalitia shackletonii	77.1223	52	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_004005475.1	s__Niallia taxi	77.0433	61	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	97.90	96.11	0.92	0.86	5	-
GCF_017303275.1	s__Cytobacillus sp017303275	76.8521	75	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002561455.1	s__Rossellomorea sp002561455	76.7859	59	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874625.1	s__Cytobacillus eiseniae	76.7318	54	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:29,936] [INFO] GTDB search result was written to GCF_002946355.1_ASM294635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:29,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:29,942] [INFO] DFAST_QC result json was written to GCF_002946355.1_ASM294635v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:29,942] [INFO] DFAST_QC completed!
[2024-01-24 12:08:29,942] [INFO] Total running time: 0h1m11s