[2024-01-24 13:22:10,691] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference
[2024-01-24 13:22:11,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,992] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf1fcf5d-a3de-4773-a42d-550f8f574d51/GCF_014635605.1_ASM1463560v1_genomic.fna.gz | prodigal -d GCF_014635605.1_ASM1463560v1_genomic.fna/cds.fna -a GCF_014635605.1_ASM1463560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:28,940] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:28,940] [INFO] Task started: HMMsearch
[2024-01-24 13:22:28,940] [INFO] Running command: hmmsearch --tblout GCF_014635605.1_ASM1463560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference/reference_markers.hmm GCF_014635605.1_ASM1463560v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:29,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:29,294] [INFO] Found 6/6 markers.
[2024-01-24 13:22:29,342] [INFO] Query marker FASTA was written to GCF_014635605.1_ASM1463560v1_genomic.fna/markers.fasta
[2024-01-24 13:22:29,342] [INFO] Task started: Blastn
[2024-01-24 13:22:29,342] [INFO] Running command: blastn -query GCF_014635605.1_ASM1463560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference/reference_markers.fasta -out GCF_014635605.1_ASM1463560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:30,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:30,037] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:30,037] [INFO] Target genome list was writen to GCF_014635605.1_ASM1463560v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:30,042] [INFO] Task started: fastANI
[2024-01-24 13:22:30,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf1fcf5d-a3de-4773-a42d-550f8f574d51/GCF_014635605.1_ASM1463560v1_genomic.fna.gz --refList GCF_014635605.1_ASM1463560v1_genomic.fna/target_genomes.txt --output GCF_014635605.1_ASM1463560v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:46,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:46,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:46,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:46,365] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:46,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:46,366] [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
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	100.0	1973	1973	95	conclusive
Saccharibacillus endophyticus	strain=CCM 8702	GCA_013185185.1	2060666	2060666	type	True	99.9973	1964	1973	95	conclusive
Saccharibacillus sacchari	strain=DSM 19268	GCA_000585395.1	456493	456493	type	True	92.4222	1743	1973	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	81.5623	1210	1973	95	below_threshold
Saccharibacillus brassicae	strain=ATSA2	GCA_006542275.1	2583377	2583377	type	True	81.4718	1209	1973	95	below_threshold
Saccharibacillus deserti	strain=KCTC 33693	GCA_013185225.1	1634444	1634444	type	True	81.1931	1117	1973	95	below_threshold
Saccharibacillus deserti	strain=WLJ055	GCA_013618475.1	1634444	1634444	type	True	81.1732	1120	1973	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	81.0644	1138	1973	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.7755	119	1973	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.6648	197	1973	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.6541	106	1973	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.4791	182	1973	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.4569	74	1973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:46,370] [INFO] DFAST Taxonomy check result was written to GCF_014635605.1_ASM1463560v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:46,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:46,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:46,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference/checkm_data
[2024-01-24 13:22:46,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:46,446] [INFO] Task started: CheckM
[2024-01-24 13:22:46,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635605.1_ASM1463560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635605.1_ASM1463560v1_genomic.fna/checkm_input GCF_014635605.1_ASM1463560v1_genomic.fna/checkm_result
[2024-01-24 13:23:34,485] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:34,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:34,510] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:34,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:34,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635605.1_ASM1463560v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:34,512] [INFO] Task started: Blastn
[2024-01-24 13:23:34,512] [INFO] Running command: blastn -query GCF_014635605.1_ASM1463560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6195fe8-ec13-43bf-ab3d-343e8533ba1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635605.1_ASM1463560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:35,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:35,450] [INFO] Selected 8 target genomes.
[2024-01-24 13:23:35,450] [INFO] Target genome list was writen to GCF_014635605.1_ASM1463560v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:35,457] [INFO] Task started: fastANI
[2024-01-24 13:23:35,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf1fcf5d-a3de-4773-a42d-550f8f574d51/GCF_014635605.1_ASM1463560v1_genomic.fna.gz --refList GCF_014635605.1_ASM1463560v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635605.1_ASM1463560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:46,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:46,563] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:46,563] [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_013185185.1	s__Saccharibacillus endophyticus	99.9973	1964	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000585395.1	s__Saccharibacillus sacchari	92.422	1743	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205895.1	s__Saccharibacillus sp002205895	81.6472	1270	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090185.1	s__Saccharibacillus alkalitolerans	81.5647	1210	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542275.1	s__Saccharibacillus brassicae	81.478	1207	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	97.06	97.06	0.95	0.95	2	-
GCF_013618475.1	s__Saccharibacillus deserti	81.1765	1120	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013185195.1	s__Saccharibacillus qingshengii	81.0664	1139	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002189105.1	s__Saccharibacillus sp002189105	79.7276	933	1973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:46,565] [INFO] GTDB search result was written to GCF_014635605.1_ASM1463560v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:46,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:46,569] [INFO] DFAST_QC result json was written to GCF_014635605.1_ASM1463560v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:46,569] [INFO] DFAST_QC completed!
[2024-01-24 13:23:46,569] [INFO] Total running time: 0h1m36s