[2024-01-24 11:43:35,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:35,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:35,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference
[2024-01-24 11:43:36,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,244] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,245] [INFO] Running command: gunzip -c /var/lib/cwl/stgd12f0afd-1de7-4965-ac17-4823fa74d1c4/GCF_016401385.1_ASM1640138v1_genomic.fna.gz | prodigal -d GCF_016401385.1_ASM1640138v1_genomic.fna/cds.fna -a GCF_016401385.1_ASM1640138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:44,632] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:44,633] [INFO] Task started: HMMsearch
[2024-01-24 11:43:44,633] [INFO] Running command: hmmsearch --tblout GCF_016401385.1_ASM1640138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference/reference_markers.hmm GCF_016401385.1_ASM1640138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:44,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:44,907] [INFO] Found 6/6 markers.
[2024-01-24 11:43:44,944] [INFO] Query marker FASTA was written to GCF_016401385.1_ASM1640138v1_genomic.fna/markers.fasta
[2024-01-24 11:43:44,945] [INFO] Task started: Blastn
[2024-01-24 11:43:44,945] [INFO] Running command: blastn -query GCF_016401385.1_ASM1640138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference/reference_markers.fasta -out GCF_016401385.1_ASM1640138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:45,535] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:45,541] [INFO] Selected 14 target genomes.
[2024-01-24 11:43:45,541] [INFO] Target genome list was writen to GCF_016401385.1_ASM1640138v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:45,659] [INFO] Task started: fastANI
[2024-01-24 11:43:45,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgd12f0afd-1de7-4965-ac17-4823fa74d1c4/GCF_016401385.1_ASM1640138v1_genomic.fna.gz --refList GCF_016401385.1_ASM1640138v1_genomic.fna/target_genomes.txt --output GCF_016401385.1_ASM1640138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:55,832] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:55,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:55,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:55,843] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:55,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:55,843] [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
Fictibacillus halophilus	strain=KCTC 33758	GCA_016401385.1	1610490	1610490	type	True	100.0	1304	1304	95	conclusive
Fictibacillus norfolkensis	strain=Sa2CUA10	GCA_014836645.1	2762233	2762233	type	True	90.6027	1122	1304	95	below_threshold
Fictibacillus barbaricus	strain=DSM 14730	GCA_017052555.1	182136	182136	type	True	82.2315	760	1304	95	below_threshold
Fictibacillus barbaricus	strain=CCM 4982	GCA_014635025.1	182136	182136	type	True	82.2031	767	1304	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	81.1213	648	1304	95	below_threshold
Fictibacillus aquaticus	strain=GDSW-R2A3	GCA_002245695.1	2021314	2021314	type	True	78.0194	173	1304	95	below_threshold
Fictibacillus solisalsi	strain=CGMCC 1.6854	GCA_900103485.1	459525	459525	type	True	77.814	109	1304	95	below_threshold
Fictibacillus enclensis	strain=NIO-1003	GCA_900094955.1	1017270	1017270	type	True	77.7728	105	1304	95	below_threshold
Fictibacillus enclensis	strain=NIO-1003	GCA_001457035.1	1017270	1017270	type	True	77.7728	105	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:55,845] [INFO] DFAST Taxonomy check result was written to GCF_016401385.1_ASM1640138v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:55,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:55,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:55,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference/checkm_data
[2024-01-24 11:43:55,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:55,883] [INFO] Task started: CheckM
[2024-01-24 11:43:55,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016401385.1_ASM1640138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016401385.1_ASM1640138v1_genomic.fna/checkm_input GCF_016401385.1_ASM1640138v1_genomic.fna/checkm_result
[2024-01-24 11:44:26,548] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:26,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:26,575] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:26,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:26,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016401385.1_ASM1640138v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:26,577] [INFO] Task started: Blastn
[2024-01-24 11:44:26,577] [INFO] Running command: blastn -query GCF_016401385.1_ASM1640138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31869735-e803-426a-be27-d51d11b61d3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016401385.1_ASM1640138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:27,354] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:27,358] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:27,358] [INFO] Target genome list was writen to GCF_016401385.1_ASM1640138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:27,376] [INFO] Task started: fastANI
[2024-01-24 11:44:27,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgd12f0afd-1de7-4965-ac17-4823fa74d1c4/GCF_016401385.1_ASM1640138v1_genomic.fna.gz --refList GCF_016401385.1_ASM1640138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016401385.1_ASM1640138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:35,652] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:35,666] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:35,666] [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_016401385.1	s__Fictibacillus halophilus	100.0	1304	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007673525.1	s__Fictibacillus phosphorivorans_C	91.3929	1167	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	98.18	98.18	0.90	0.90	2	-
GCA_017052515.1	s__Fictibacillus nanhaiensis_B	90.622	1135	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836645.1	s__Fictibacillus sp014836645	90.6027	1122	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016401345.1	s__Fictibacillus nanhaiensis_A	90.571	1126	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	97.66	97.26	0.91	0.88	5	-
GCF_005503015.1	s__Fictibacillus sp005503015	90.2421	1162	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001629705.1	s__Fictibacillus phosphorivorans_A	90.0281	1151	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	97.31	97.31	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,668] [INFO] GTDB search result was written to GCF_016401385.1_ASM1640138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:35,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:35,673] [INFO] DFAST_QC result json was written to GCF_016401385.1_ASM1640138v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:35,673] [INFO] DFAST_QC completed!
[2024-01-24 11:44:35,674] [INFO] Total running time: 0h1m1s