[2024-01-24 12:37:09,703] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,707] [INFO] DQC Reference Directory: /var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference
[2024-01-24 12:37:11,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,026] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c48e820-4c71-4d9d-ba61-2b578507acb9/GCF_026547225.1_ASM2654722v1_genomic.fna.gz | prodigal -d GCF_026547225.1_ASM2654722v1_genomic.fna/cds.fna -a GCF_026547225.1_ASM2654722v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:18,307] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:18,307] [INFO] Task started: HMMsearch
[2024-01-24 12:37:18,308] [INFO] Running command: hmmsearch --tblout GCF_026547225.1_ASM2654722v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference/reference_markers.hmm GCF_026547225.1_ASM2654722v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:18,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:18,593] [INFO] Found 6/6 markers.
[2024-01-24 12:37:18,626] [INFO] Query marker FASTA was written to GCF_026547225.1_ASM2654722v1_genomic.fna/markers.fasta
[2024-01-24 12:37:18,627] [INFO] Task started: Blastn
[2024-01-24 12:37:18,627] [INFO] Running command: blastn -query GCF_026547225.1_ASM2654722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference/reference_markers.fasta -out GCF_026547225.1_ASM2654722v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:19,199] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:19,202] [INFO] Selected 28 target genomes.
[2024-01-24 12:37:19,203] [INFO] Target genome list was writen to GCF_026547225.1_ASM2654722v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:19,231] [INFO] Task started: fastANI
[2024-01-24 12:37:19,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c48e820-4c71-4d9d-ba61-2b578507acb9/GCF_026547225.1_ASM2654722v1_genomic.fna.gz --refList GCF_026547225.1_ASM2654722v1_genomic.fna/target_genomes.txt --output GCF_026547225.1_ASM2654722v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:35,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:35,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:35,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:35,531] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:35,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:35,531] [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
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	79.2356	50	1050	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	78.6996	53	1050	95	below_threshold
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	78.4665	85	1050	95	below_threshold
Caldibacillus pasinlerensis	strain=P1	GCA_009996845.1	2703818	2703818	type	True	76.9558	89	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:35,533] [INFO] DFAST Taxonomy check result was written to GCF_026547225.1_ASM2654722v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:35,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:35,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:35,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference/checkm_data
[2024-01-24 12:37:35,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:35,573] [INFO] Task started: CheckM
[2024-01-24 12:37:35,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026547225.1_ASM2654722v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026547225.1_ASM2654722v1_genomic.fna/checkm_input GCF_026547225.1_ASM2654722v1_genomic.fna/checkm_result
[2024-01-24 12:38:03,320] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:03,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,344] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:03,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:03,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026547225.1_ASM2654722v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:03,345] [INFO] Task started: Blastn
[2024-01-24 12:38:03,346] [INFO] Running command: blastn -query GCF_026547225.1_ASM2654722v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedee0689-5dd3-47a3-8c48-f4ac05ea9d36/dqc_reference/reference_markers_gtdb.fasta -out GCF_026547225.1_ASM2654722v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:04,103] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:04,108] [INFO] Selected 31 target genomes.
[2024-01-24 12:38:04,108] [INFO] Target genome list was writen to GCF_026547225.1_ASM2654722v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:04,160] [INFO] Task started: fastANI
[2024-01-24 12:38:04,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c48e820-4c71-4d9d-ba61-2b578507acb9/GCF_026547225.1_ASM2654722v1_genomic.fna.gz --refList GCF_026547225.1_ASM2654722v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026547225.1_ASM2654722v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:25,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:25,553] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:38:25,554] [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_001420715.1	s__Margalitia shackletonii	79.5243	52	1050	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_003688615.2	s__Parageobacillus toebii	79.4724	51	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_000262755.1	s__Bacillus_Z methanolicus	79.1395	55	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001645685.2	s__Peribacillus muralis_A	78.5616	50	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244735.1	s__Bacillus_J andreraoultii	78.4776	85	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_000751775.1	s__Bacillus_J thermoamylovorans	77.4183	94	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	98.31	97.86	0.86	0.85	9	-
GCF_009996845.1	s__RUG14133 sp009996845	76.9558	89	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__RUG14133	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341205.1	s__Thermolongibacillus altinsuensis	76.5843	57	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Thermolongibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,555] [INFO] GTDB search result was written to GCF_026547225.1_ASM2654722v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:25,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:25,558] [INFO] DFAST_QC result json was written to GCF_026547225.1_ASM2654722v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:25,559] [INFO] DFAST_QC completed!
[2024-01-24 12:38:25,559] [INFO] Total running time: 0h1m16s