[2024-01-24 13:13:23,615] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference
[2024-01-24 13:13:24,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:24,927] [INFO] Task started: Prodigal
[2024-01-24 13:13:24,927] [INFO] Running command: gunzip -c /var/lib/cwl/stg3753bb84-4468-4099-b317-856dde33da97/GCF_013185225.1_ASM1318522v1_genomic.fna.gz | prodigal -d GCF_013185225.1_ASM1318522v1_genomic.fna/cds.fna -a GCF_013185225.1_ASM1318522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:39,354] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:39,355] [INFO] Task started: HMMsearch
[2024-01-24 13:13:39,355] [INFO] Running command: hmmsearch --tblout GCF_013185225.1_ASM1318522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference/reference_markers.hmm GCF_013185225.1_ASM1318522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:39,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:39,732] [INFO] Found 6/6 markers.
[2024-01-24 13:13:39,774] [INFO] Query marker FASTA was written to GCF_013185225.1_ASM1318522v1_genomic.fna/markers.fasta
[2024-01-24 13:13:39,775] [INFO] Task started: Blastn
[2024-01-24 13:13:39,775] [INFO] Running command: blastn -query GCF_013185225.1_ASM1318522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference/reference_markers.fasta -out GCF_013185225.1_ASM1318522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:40,528] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:40,532] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:40,532] [INFO] Target genome list was writen to GCF_013185225.1_ASM1318522v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:40,572] [INFO] Task started: fastANI
[2024-01-24 13:13:40,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg3753bb84-4468-4099-b317-856dde33da97/GCF_013185225.1_ASM1318522v1_genomic.fna.gz --refList GCF_013185225.1_ASM1318522v1_genomic.fna/target_genomes.txt --output GCF_013185225.1_ASM1318522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:54,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:54,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:54,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:54,275] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:54,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:54,276] [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 deserti	strain=KCTC 33693	GCA_013185225.1	1634444	1634444	type	True	100.0	1698	1699	95	conclusive
Saccharibacillus deserti	strain=WLJ055	GCA_013618475.1	1634444	1634444	type	True	100.0	1698	1699	95	conclusive
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	94.6699	1483	1699	95	below_threshold
Saccharibacillus brassicae	strain=ATSA2	GCA_006542275.1	2583377	2583377	type	True	85.0519	1347	1699	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	82.0959	1231	1699	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	81.1929	1130	1699	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9386	212	1699	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	76.8438	102	1699	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.8426	146	1699	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.6506	190	1699	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.2801	93	1699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:54,278] [INFO] DFAST Taxonomy check result was written to GCF_013185225.1_ASM1318522v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:54,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:54,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:54,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference/checkm_data
[2024-01-24 13:13:54,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:54,331] [INFO] Task started: CheckM
[2024-01-24 13:13:54,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013185225.1_ASM1318522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013185225.1_ASM1318522v1_genomic.fna/checkm_input GCF_013185225.1_ASM1318522v1_genomic.fna/checkm_result
[2024-01-24 13:14:38,615] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:38,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:38,639] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:38,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:38,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013185225.1_ASM1318522v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:38,640] [INFO] Task started: Blastn
[2024-01-24 13:14:38,641] [INFO] Running command: blastn -query GCF_013185225.1_ASM1318522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8116d141-93a7-4edb-bd2f-33ce362b6bef/dqc_reference/reference_markers_gtdb.fasta -out GCF_013185225.1_ASM1318522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:39,599] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:39,603] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:39,603] [INFO] Target genome list was writen to GCF_013185225.1_ASM1318522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:39,613] [INFO] Task started: fastANI
[2024-01-24 13:14:39,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg3753bb84-4468-4099-b317-856dde33da97/GCF_013185225.1_ASM1318522v1_genomic.fna.gz --refList GCF_013185225.1_ASM1318522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013185225.1_ASM1318522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:51,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:51,460] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:51,460] [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_013618475.1	s__Saccharibacillus deserti	100.0	1698	1699	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_013185195.1	s__Saccharibacillus qingshengii	94.6699	1483	1699	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	85.0519	1347	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	97.06	97.06	0.95	0.95	2	-
GCF_011090185.1	s__Saccharibacillus alkalitolerans	82.0895	1232	1699	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	81.3353	1215	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185185.1	s__Saccharibacillus endophyticus	81.1263	1143	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000585395.1	s__Saccharibacillus sacchari	81.0751	1097	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378145.1	s__Saccharibacillus kuerlensis	80.4709	932	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:51,462] [INFO] GTDB search result was written to GCF_013185225.1_ASM1318522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:51,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:51,465] [INFO] DFAST_QC result json was written to GCF_013185225.1_ASM1318522v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:51,466] [INFO] DFAST_QC completed!
[2024-01-24 13:14:51,466] [INFO] Total running time: 0h1m28s