[2024-01-24 12:37:09,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,772] [INFO] DQC Reference Directory: /var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference
[2024-01-24 12:37:11,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,062] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgc87019ca-9cbb-491b-8c09-f714361a0bd2/GCF_002874535.1_ASM287453v1_genomic.fna.gz | prodigal -d GCF_002874535.1_ASM287453v1_genomic.fna/cds.fna -a GCF_002874535.1_ASM287453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:22,508] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:22,509] [INFO] Task started: HMMsearch
[2024-01-24 12:37:22,509] [INFO] Running command: hmmsearch --tblout GCF_002874535.1_ASM287453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference/reference_markers.hmm GCF_002874535.1_ASM287453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:22,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:22,812] [INFO] Found 6/6 markers.
[2024-01-24 12:37:22,858] [INFO] Query marker FASTA was written to GCF_002874535.1_ASM287453v1_genomic.fna/markers.fasta
[2024-01-24 12:37:22,859] [INFO] Task started: Blastn
[2024-01-24 12:37:22,859] [INFO] Running command: blastn -query GCF_002874535.1_ASM287453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference/reference_markers.fasta -out GCF_002874535.1_ASM287453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:23,462] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:23,468] [INFO] Selected 9 target genomes.
[2024-01-24 12:37:23,468] [INFO] Target genome list was writen to GCF_002874535.1_ASM287453v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:23,474] [INFO] Task started: fastANI
[2024-01-24 12:37:23,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgc87019ca-9cbb-491b-8c09-f714361a0bd2/GCF_002874535.1_ASM287453v1_genomic.fna.gz --refList GCF_002874535.1_ASM287453v1_genomic.fna/target_genomes.txt --output GCF_002874535.1_ASM287453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:33,326] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:33,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:33,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:33,334] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:33,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:33,334] [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
Mesobacillus jeotgali	strain=DSM 18226	GCA_002874535.1	129985	129985	type	True	100.0	1565	1567	95	conclusive
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	91.263	1293	1567	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_000517385.1	308892	308892	type	True	90.2481	1105	1567	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_001315165.1	308892	308892	type	True	90.248	1105	1567	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	81.6966	915	1567	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.6835	137	1567	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.983	68	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:33,336] [INFO] DFAST Taxonomy check result was written to GCF_002874535.1_ASM287453v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:33,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:33,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:33,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference/checkm_data
[2024-01-24 12:37:33,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:33,387] [INFO] Task started: CheckM
[2024-01-24 12:37:33,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002874535.1_ASM287453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002874535.1_ASM287453v1_genomic.fna/checkm_input GCF_002874535.1_ASM287453v1_genomic.fna/checkm_result
[2024-01-24 12:38:11,720] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:11,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:11,746] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:11,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:11,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002874535.1_ASM287453v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:11,747] [INFO] Task started: Blastn
[2024-01-24 12:38:11,747] [INFO] Running command: blastn -query GCF_002874535.1_ASM287453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc133280d-0a09-49e4-9abc-43b9ad6b3efb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002874535.1_ASM287453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:12,526] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:12,530] [INFO] Selected 8 target genomes.
[2024-01-24 12:38:12,531] [INFO] Target genome list was writen to GCF_002874535.1_ASM287453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:12,542] [INFO] Task started: fastANI
[2024-01-24 12:38:12,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgc87019ca-9cbb-491b-8c09-f714361a0bd2/GCF_002874535.1_ASM287453v1_genomic.fna.gz --refList GCF_002874535.1_ASM287453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002874535.1_ASM287453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:23,414] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:23,430] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:23,431] [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_002874535.1	s__Mesobacillus jeotgali	100.0	1564	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018613315.1	s__Mesobacillus sp018613315	91.318	1278	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813125.1	s__Mesobacillus selenatarsenatis	91.2473	1295	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613155.1	s__Mesobacillus sp018613155	90.6103	1220	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000517385.1	s__Mesobacillus boroniphilus	90.2481	1105	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	99.96	99.92	1.00	0.99	3	-
GCF_018424685.1	s__Mesobacillus boroniphilus_A	88.179	1219	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613235.1	s__Mesobacillus sp018613235	86.8792	1146	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014856545.1	s__Mesobacillus sp014856545	86.8609	1193	1567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:23,433] [INFO] GTDB search result was written to GCF_002874535.1_ASM287453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:23,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:23,439] [INFO] DFAST_QC result json was written to GCF_002874535.1_ASM287453v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:23,439] [INFO] DFAST_QC completed!
[2024-01-24 12:38:23,439] [INFO] Total running time: 0h1m14s