[2024-01-24 13:13:35,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:35,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:35,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference
[2024-01-24 13:13:36,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:36,261] [INFO] Task started: Prodigal
[2024-01-24 13:13:36,261] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe1cd3d0-0b36-4419-8e26-fcfd081970ab/GCF_003710905.1_ASM371090v1_genomic.fna.gz | prodigal -d GCF_003710905.1_ASM371090v1_genomic.fna/cds.fna -a GCF_003710905.1_ASM371090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:00,443] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:00,444] [INFO] Task started: HMMsearch
[2024-01-24 13:14:00,444] [INFO] Running command: hmmsearch --tblout GCF_003710905.1_ASM371090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference/reference_markers.hmm GCF_003710905.1_ASM371090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:00,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:00,730] [INFO] Found 6/6 markers.
[2024-01-24 13:14:00,779] [INFO] Query marker FASTA was written to GCF_003710905.1_ASM371090v1_genomic.fna/markers.fasta
[2024-01-24 13:14:00,779] [INFO] Task started: Blastn
[2024-01-24 13:14:00,779] [INFO] Running command: blastn -query GCF_003710905.1_ASM371090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference/reference_markers.fasta -out GCF_003710905.1_ASM371090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:01,417] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:01,421] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:01,422] [INFO] Target genome list was writen to GCF_003710905.1_ASM371090v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:01,442] [INFO] Task started: fastANI
[2024-01-24 13:14:01,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe1cd3d0-0b36-4419-8e26-fcfd081970ab/GCF_003710905.1_ASM371090v1_genomic.fna.gz --refList GCF_003710905.1_ASM371090v1_genomic.fna/target_genomes.txt --output GCF_003710905.1_ASM371090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:11,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:11,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:11,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:11,323] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:11,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:11,323] [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
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	100.0	1998	1999	95	conclusive
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	99.9774	1925	1999	95	conclusive
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	85.3712	1391	1999	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	85.3566	1377	1999	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	85.316	1359	1999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:11,325] [INFO] DFAST Taxonomy check result was written to GCF_003710905.1_ASM371090v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:11,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:11,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:11,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference/checkm_data
[2024-01-24 13:14:11,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:11,380] [INFO] Task started: CheckM
[2024-01-24 13:14:11,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710905.1_ASM371090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710905.1_ASM371090v1_genomic.fna/checkm_input GCF_003710905.1_ASM371090v1_genomic.fna/checkm_result
[2024-01-24 13:15:18,296] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:18,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:18,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:18,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:18,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710905.1_ASM371090v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:18,318] [INFO] Task started: Blastn
[2024-01-24 13:15:18,318] [INFO] Running command: blastn -query GCF_003710905.1_ASM371090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408e0086-1b0d-4c19-87ba-aa5f9d102059/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710905.1_ASM371090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:19,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:19,206] [INFO] Selected 13 target genomes.
[2024-01-24 13:15:19,206] [INFO] Target genome list was writen to GCF_003710905.1_ASM371090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:19,245] [INFO] Task started: fastANI
[2024-01-24 13:15:19,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe1cd3d0-0b36-4419-8e26-fcfd081970ab/GCF_003710905.1_ASM371090v1_genomic.fna.gz --refList GCF_003710905.1_ASM371090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710905.1_ASM371090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:35,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:35,383] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:35,383] [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_003710905.1	s__Brevibacillus parabrevis	100.0	1998	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	conclusive
GCF_004117055.1	s__Brevibacillus agri	85.3663	1392	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_003710935.1	s__Brevibacillus gelatini	84.0741	1170	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013475.1	s__Brevibacillus porteri	80.4856	865	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_005217615.1	s__Brevibacillus antibioticus	80.3518	843	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282075.1	s__Brevibacillus sp000282075	80.3188	871	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_013284355.1	s__Brevibacillus sp013284355	80.3098	884	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039275.2	s__Brevibacillus brevis_C	80.2977	919	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_003013405.1	s__Brevibacillus formosus	80.2913	886	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_000010165.1	s__Brevibacillus brevis_D	80.2675	885	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	79.9862	776	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_001420695.1	s__Brevibacillus choshinensis	79.7914	657	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	79.7659	710	1999	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:35,385] [INFO] GTDB search result was written to GCF_003710905.1_ASM371090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:35,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:35,389] [INFO] DFAST_QC result json was written to GCF_003710905.1_ASM371090v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:35,389] [INFO] DFAST_QC completed!
[2024-01-24 13:15:35,389] [INFO] Total running time: 0h2m0s