[2024-01-25 19:03:05,615] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:05,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:05,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference
[2024-01-25 19:03:06,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:06,699] [INFO] Task started: Prodigal
[2024-01-25 19:03:06,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg4027b3d3-27bc-442a-aaad-db56797f92a0/GCF_014645255.1_ASM1464525v1_genomic.fna.gz | prodigal -d GCF_014645255.1_ASM1464525v1_genomic.fna/cds.fna -a GCF_014645255.1_ASM1464525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:17,692] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:17,692] [INFO] Task started: HMMsearch
[2024-01-25 19:03:17,692] [INFO] Running command: hmmsearch --tblout GCF_014645255.1_ASM1464525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference/reference_markers.hmm GCF_014645255.1_ASM1464525v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:17,930] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:17,931] [INFO] Found 6/6 markers.
[2024-01-25 19:03:17,969] [INFO] Query marker FASTA was written to GCF_014645255.1_ASM1464525v1_genomic.fna/markers.fasta
[2024-01-25 19:03:17,969] [INFO] Task started: Blastn
[2024-01-25 19:03:17,969] [INFO] Running command: blastn -query GCF_014645255.1_ASM1464525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference/reference_markers.fasta -out GCF_014645255.1_ASM1464525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:18,591] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:18,594] [INFO] Selected 14 target genomes.
[2024-01-25 19:03:18,594] [INFO] Target genome list was writen to GCF_014645255.1_ASM1464525v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:18,611] [INFO] Task started: fastANI
[2024-01-25 19:03:18,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg4027b3d3-27bc-442a-aaad-db56797f92a0/GCF_014645255.1_ASM1464525v1_genomic.fna.gz --refList GCF_014645255.1_ASM1464525v1_genomic.fna/target_genomes.txt --output GCF_014645255.1_ASM1464525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:33,768] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:33,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:33,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:33,779] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:03:33,779] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:33,779] [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 kuerlensis	strain=CGMCC 1.6964	GCA_014645255.1	459527	459527	type	True	100.0	1557	1560	95	conclusive
Saccharibacillus kuerlensis	strain=DSM 22868	GCA_000378145.1	459527	459527	type	True	99.9753	1524	1560	95	conclusive
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	80.9334	1027	1560	95	below_threshold
Saccharibacillus deserti	strain=WLJ055	GCA_013618475.1	1634444	1634444	type	True	80.509	911	1560	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	80.421	867	1560	95	below_threshold
Saccharibacillus brassicae	strain=ATSA2	GCA_006542275.1	2583377	2583377	type	True	80.3198	915	1560	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	79.8865	837	1560	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_013185185.1	2060666	2060666	type	True	79.8721	847	1560	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.0178	66	1560	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.8991	105	1560	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	76.6769	76	1560	95	below_threshold
Paenibacillus hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	76.6125	122	1560	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.5963	87	1560	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.4721	79	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:33,784] [INFO] DFAST Taxonomy check result was written to GCF_014645255.1_ASM1464525v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:33,785] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:33,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:33,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference/checkm_data
[2024-01-25 19:03:33,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:33,842] [INFO] Task started: CheckM
[2024-01-25 19:03:33,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645255.1_ASM1464525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645255.1_ASM1464525v1_genomic.fna/checkm_input GCF_014645255.1_ASM1464525v1_genomic.fna/checkm_result
[2024-01-25 19:04:08,582] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:08,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:08,600] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:08,600] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:08,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645255.1_ASM1464525v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:08,601] [INFO] Task started: Blastn
[2024-01-25 19:04:08,601] [INFO] Running command: blastn -query GCF_014645255.1_ASM1464525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f4c8f9e-7000-4ccb-b839-75a658d9f393/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645255.1_ASM1464525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:09,691] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:09,694] [INFO] Selected 9 target genomes.
[2024-01-25 19:04:09,694] [INFO] Target genome list was writen to GCF_014645255.1_ASM1464525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:09,703] [INFO] Task started: fastANI
[2024-01-25 19:04:09,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg4027b3d3-27bc-442a-aaad-db56797f92a0/GCF_014645255.1_ASM1464525v1_genomic.fna.gz --refList GCF_014645255.1_ASM1464525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645255.1_ASM1464525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:20,350] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:20,358] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:20,358] [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_000378145.1	s__Saccharibacillus kuerlensis	99.9753	1524	1560	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_011090185.1	s__Saccharibacillus alkalitolerans	80.9458	1025	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013618475.1	s__Saccharibacillus deserti	80.5024	912	1560	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	80.4171	868	1560	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	80.3296	913	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	97.06	97.06	0.95	0.95	2	-
GCF_002205895.1	s__Saccharibacillus sp002205895	80.0007	841	1560	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	79.8737	847	1560	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	79.7851	833	1560	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	79.4723	711	1560	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:20,359] [INFO] GTDB search result was written to GCF_014645255.1_ASM1464525v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:20,360] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:20,366] [INFO] DFAST_QC result json was written to GCF_014645255.1_ASM1464525v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:20,366] [INFO] DFAST_QC completed!
[2024-01-25 19:04:20,366] [INFO] Total running time: 0h1m15s