[2024-01-25 18:45:35,526] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:35,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:35,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference
[2024-01-25 18:45:36,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:36,727] [INFO] Task started: Prodigal
[2024-01-25 18:45:36,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg774de409-f585-4124-bce2-89ee46dd9a28/GCF_030815225.1_ASM3081522v1_genomic.fna.gz | prodigal -d GCF_030815225.1_ASM3081522v1_genomic.fna/cds.fna -a GCF_030815225.1_ASM3081522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:44,458] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:44,459] [INFO] Task started: HMMsearch
[2024-01-25 18:45:44,459] [INFO] Running command: hmmsearch --tblout GCF_030815225.1_ASM3081522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference/reference_markers.hmm GCF_030815225.1_ASM3081522v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:44,684] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:44,685] [INFO] Found 6/6 markers.
[2024-01-25 18:45:44,718] [INFO] Query marker FASTA was written to GCF_030815225.1_ASM3081522v1_genomic.fna/markers.fasta
[2024-01-25 18:45:44,718] [INFO] Task started: Blastn
[2024-01-25 18:45:44,718] [INFO] Running command: blastn -query GCF_030815225.1_ASM3081522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference/reference_markers.fasta -out GCF_030815225.1_ASM3081522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:45,252] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:45,256] [INFO] Selected 29 target genomes.
[2024-01-25 18:45:45,257] [INFO] Target genome list was writen to GCF_030815225.1_ASM3081522v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:45,298] [INFO] Task started: fastANI
[2024-01-25 18:45:45,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg774de409-f585-4124-bce2-89ee46dd9a28/GCF_030815225.1_ASM3081522v1_genomic.fna.gz --refList GCF_030815225.1_ASM3081522v1_genomic.fna/target_genomes.txt --output GCF_030815225.1_ASM3081522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:07,511] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:07,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:07,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:07,518] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:07,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:07,518] [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
Alkalihalobacillus macyae	strain=DSM 16346	GCA_001039475.1	157733	157733	type	True	96.3904	1254	1361	95	conclusive
Fictibacillus macauensis	strain=ZFHKF-1	GCA_000269865.1	245160	245160	type	True	76.9448	55	1361	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.6541	52	1361	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	76.5266	68	1361	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	76.352	50	1361	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	76.1489	51	1361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:07,519] [INFO] DFAST Taxonomy check result was written to GCF_030815225.1_ASM3081522v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:07,520] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:07,520] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:07,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference/checkm_data
[2024-01-25 18:46:07,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:07,562] [INFO] Task started: CheckM
[2024-01-25 18:46:07,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030815225.1_ASM3081522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030815225.1_ASM3081522v1_genomic.fna/checkm_input GCF_030815225.1_ASM3081522v1_genomic.fna/checkm_result
[2024-01-25 18:46:34,932] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:34,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:34,989] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:34,989] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:34,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030815225.1_ASM3081522v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:34,990] [INFO] Task started: Blastn
[2024-01-25 18:46:34,990] [INFO] Running command: blastn -query GCF_030815225.1_ASM3081522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec3e053-a6e5-4387-be63-7775fcb92d36/dqc_reference/reference_markers_gtdb.fasta -out GCF_030815225.1_ASM3081522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:35,783] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:35,785] [INFO] Selected 8 target genomes.
[2024-01-25 18:46:35,786] [INFO] Target genome list was writen to GCF_030815225.1_ASM3081522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:35,797] [INFO] Task started: fastANI
[2024-01-25 18:46:35,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg774de409-f585-4124-bce2-89ee46dd9a28/GCF_030815225.1_ASM3081522v1_genomic.fna.gz --refList GCF_030815225.1_ASM3081522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030815225.1_ASM3081522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:44,991] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:44,997] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:44,997] [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_001039475.1	s__Anaerobacillus_A macyae	96.3873	1254	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005144865.1	s__Anaerobacillus_A hwajinpoensis_A	87.3913	1148	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303315.1	s__Anaerobacillus_A sp017303315	87.2513	1118	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009818105.1	s__Anaerobacillus_A sp009818105	80.908	693	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234585.1	s__Anaerobacillus_A hwajinpoensis_B	80.8973	695	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563635.1	s__Anaerobacillus_A sp002563635	80.7179	712	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	96.09	95.80	0.90	0.90	3	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	76.4592	52	1361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:44,999] [INFO] GTDB search result was written to GCF_030815225.1_ASM3081522v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:44,999] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:45,001] [INFO] DFAST_QC result json was written to GCF_030815225.1_ASM3081522v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:45,001] [INFO] DFAST_QC completed!
[2024-01-25 18:46:45,001] [INFO] Total running time: 0h1m9s