[2024-01-24 12:39:40,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:40,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:40,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference
[2024-01-24 12:39:41,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:41,632] [INFO] Task started: Prodigal
[2024-01-24 12:39:41,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg31b3b467-fafb-4021-90ab-052764197a8b/GCF_009650095.1_ASM965009v1_genomic.fna.gz | prodigal -d GCF_009650095.1_ASM965009v1_genomic.fna/cds.fna -a GCF_009650095.1_ASM965009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:52,267] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:52,268] [INFO] Task started: HMMsearch
[2024-01-24 12:39:52,268] [INFO] Running command: hmmsearch --tblout GCF_009650095.1_ASM965009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference/reference_markers.hmm GCF_009650095.1_ASM965009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:52,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:52,603] [INFO] Found 6/6 markers.
[2024-01-24 12:39:52,650] [INFO] Query marker FASTA was written to GCF_009650095.1_ASM965009v1_genomic.fna/markers.fasta
[2024-01-24 12:39:52,650] [INFO] Task started: Blastn
[2024-01-24 12:39:52,650] [INFO] Running command: blastn -query GCF_009650095.1_ASM965009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference/reference_markers.fasta -out GCF_009650095.1_ASM965009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:53,282] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:53,286] [INFO] Selected 10 target genomes.
[2024-01-24 12:39:53,286] [INFO] Target genome list was writen to GCF_009650095.1_ASM965009v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:53,293] [INFO] Task started: fastANI
[2024-01-24 12:39:53,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg31b3b467-fafb-4021-90ab-052764197a8b/GCF_009650095.1_ASM965009v1_genomic.fna.gz --refList GCF_009650095.1_ASM965009v1_genomic.fna/target_genomes.txt --output GCF_009650095.1_ASM965009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:03,965] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:03,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:03,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:03,974] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:03,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:03,975] [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
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	100.0	1696	1696	95	conclusive
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	87.1284	1205	1696	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	85.7047	1123	1696	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	85.5248	1108	1696	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	85.4847	1021	1696	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	85.4227	1016	1696	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	85.4199	1083	1696	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	78.3387	73	1696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:03,979] [INFO] DFAST Taxonomy check result was written to GCF_009650095.1_ASM965009v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:03,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:03,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:03,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference/checkm_data
[2024-01-24 12:40:03,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:04,036] [INFO] Task started: CheckM
[2024-01-24 12:40:04,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009650095.1_ASM965009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009650095.1_ASM965009v1_genomic.fna/checkm_input GCF_009650095.1_ASM965009v1_genomic.fna/checkm_result
[2024-01-24 12:40:41,475] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:41,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,510] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:41,510] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:41,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009650095.1_ASM965009v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:41,511] [INFO] Task started: Blastn
[2024-01-24 12:40:41,512] [INFO] Running command: blastn -query GCF_009650095.1_ASM965009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f20a346-ff94-414e-ab30-d5b87382a8b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009650095.1_ASM965009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:42,297] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:42,302] [INFO] Selected 8 target genomes.
[2024-01-24 12:40:42,302] [INFO] Target genome list was writen to GCF_009650095.1_ASM965009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:42,309] [INFO] Task started: fastANI
[2024-01-24 12:40:42,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg31b3b467-fafb-4021-90ab-052764197a8b/GCF_009650095.1_ASM965009v1_genomic.fna.gz --refList GCF_009650095.1_ASM965009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009650095.1_ASM965009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:51,793] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:51,806] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:51,806] [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_009650095.1	s__Gracilibacillus sp002797295	100.0	1696	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	conclusive
GCF_900114645.1	s__Gracilibacillus orientalis	87.1074	1207	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599345.1	s__Gracilibacillus sp017599345	85.7098	1122	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	85.5362	1106	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_900143085.1	s__Gracilibacillus kekensis	79.2369	519	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	79.1445	543	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521485.1	s__Gracilibacillus boraciitolerans	78.6816	418	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612345.1	s__Virgibacillus sp003612345	76.6015	64	1696	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:51,808] [INFO] GTDB search result was written to GCF_009650095.1_ASM965009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:51,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:51,812] [INFO] DFAST_QC result json was written to GCF_009650095.1_ASM965009v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:51,812] [INFO] DFAST_QC completed!
[2024-01-24 12:40:51,812] [INFO] Total running time: 0h1m11s