[2024-01-24 13:19:25,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference
[2024-01-24 13:19:27,234] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,235] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg8340ab11-7ca6-4b42-993c-af8d60172843/GCF_013618475.1_ASM1361847v1_genomic.fna.gz | prodigal -d GCF_013618475.1_ASM1361847v1_genomic.fna/cds.fna -a GCF_013618475.1_ASM1361847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:40,861] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:40,862] [INFO] Task started: HMMsearch
[2024-01-24 13:19:40,862] [INFO] Running command: hmmsearch --tblout GCF_013618475.1_ASM1361847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference/reference_markers.hmm GCF_013618475.1_ASM1361847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:41,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:41,160] [INFO] Found 6/6 markers.
[2024-01-24 13:19:41,200] [INFO] Query marker FASTA was written to GCF_013618475.1_ASM1361847v1_genomic.fna/markers.fasta
[2024-01-24 13:19:41,200] [INFO] Task started: Blastn
[2024-01-24 13:19:41,200] [INFO] Running command: blastn -query GCF_013618475.1_ASM1361847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference/reference_markers.fasta -out GCF_013618475.1_ASM1361847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:41,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:41,814] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:41,815] [INFO] Target genome list was writen to GCF_013618475.1_ASM1361847v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:41,824] [INFO] Task started: fastANI
[2024-01-24 13:19:41,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg8340ab11-7ca6-4b42-993c-af8d60172843/GCF_013618475.1_ASM1361847v1_genomic.fna.gz --refList GCF_013618475.1_ASM1361847v1_genomic.fna/target_genomes.txt --output GCF_013618475.1_ASM1361847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:54,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:54,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:54,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:54,961] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:54,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:54,962] [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=WLJ055	GCA_013618475.1	1634444	1634444	type	True	100.0	1698	1699	95	conclusive
Saccharibacillus deserti	strain=KCTC 33693	GCA_013185225.1	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	85.0459	1348	1699	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	82.0897	1232	1699	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	81.1948	1128	1699	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9576	213	1699	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	76.8837	103	1699	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.8492	146	1699	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.6515	190	1699	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.2818	93	1699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:54,963] [INFO] DFAST Taxonomy check result was written to GCF_013618475.1_ASM1361847v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:54,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:54,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:54,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference/checkm_data
[2024-01-24 13:19:54,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:55,016] [INFO] Task started: CheckM
[2024-01-24 13:19:55,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013618475.1_ASM1361847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013618475.1_ASM1361847v1_genomic.fna/checkm_input GCF_013618475.1_ASM1361847v1_genomic.fna/checkm_result
[2024-01-24 13:20:36,072] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:36,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:36,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:36,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:36,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013618475.1_ASM1361847v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:36,096] [INFO] Task started: Blastn
[2024-01-24 13:20:36,096] [INFO] Running command: blastn -query GCF_013618475.1_ASM1361847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a658a00-ec5c-4b28-b8b3-cfa87a3ac712/dqc_reference/reference_markers_gtdb.fasta -out GCF_013618475.1_ASM1361847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:36,911] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:36,916] [INFO] Selected 8 target genomes.
[2024-01-24 13:20:36,916] [INFO] Target genome list was writen to GCF_013618475.1_ASM1361847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:36,937] [INFO] Task started: fastANI
[2024-01-24 13:20:36,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg8340ab11-7ca6-4b42-993c-af8d60172843/GCF_013618475.1_ASM1361847v1_genomic.fna.gz --refList GCF_013618475.1_ASM1361847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013618475.1_ASM1361847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:47,003] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:47,018] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:47,018] [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	85.0459	1348	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	82.0775	1234	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	81.3294	1216	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	81.1237	1144	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	81.0774	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	80.4748	933	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 13:20:47,020] [INFO] GTDB search result was written to GCF_013618475.1_ASM1361847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:47,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:47,023] [INFO] DFAST_QC result json was written to GCF_013618475.1_ASM1361847v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:47,023] [INFO] DFAST_QC completed!
[2024-01-24 13:20:47,023] [INFO] Total running time: 0h1m21s