[2024-01-24 13:40:43,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference
[2024-01-24 13:40:44,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,906] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ea329a1-bd1e-4ad9-a012-ce52988daba8/GCF_003315295.1_ASM331529v1_genomic.fna.gz | prodigal -d GCF_003315295.1_ASM331529v1_genomic.fna/cds.fna -a GCF_003315295.1_ASM331529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:51,367] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:51,368] [INFO] Task started: HMMsearch
[2024-01-24 13:40:51,368] [INFO] Running command: hmmsearch --tblout GCF_003315295.1_ASM331529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference/reference_markers.hmm GCF_003315295.1_ASM331529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,646] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,647] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,673] [INFO] Query marker FASTA was written to GCF_003315295.1_ASM331529v1_genomic.fna/markers.fasta
[2024-01-24 13:40:51,674] [INFO] Task started: Blastn
[2024-01-24 13:40:51,674] [INFO] Running command: blastn -query GCF_003315295.1_ASM331529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference/reference_markers.fasta -out GCF_003315295.1_ASM331529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,305] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,309] [INFO] Selected 20 target genomes.
[2024-01-24 13:40:52,310] [INFO] Target genome list was writen to GCF_003315295.1_ASM331529v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,321] [INFO] Task started: fastANI
[2024-01-24 13:40:52,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea329a1-bd1e-4ad9-a012-ce52988daba8/GCF_003315295.1_ASM331529v1_genomic.fna.gz --refList GCF_003315295.1_ASM331529v1_genomic.fna/target_genomes.txt --output GCF_003315295.1_ASM331529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,518] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,530] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:04,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:04,530] [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
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	100.0	1015	1017	95	conclusive
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	78.2219	270	1017	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	78.1918	73	1017	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	77.8978	92	1017	95	below_threshold
Amphibacillus cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	77.8233	110	1017	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.7845	197	1017	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	77.77	194	1017	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.7643	111	1017	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.5946	213	1017	95	below_threshold
Amphibacillus jilinensis	strain=Y1	GCA_000306965.1	1216008	1216008	type	True	77.5769	111	1017	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.1773	127	1017	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	77.1674	151	1017	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.132	99	1017	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.8506	109	1017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,534] [INFO] DFAST Taxonomy check result was written to GCF_003315295.1_ASM331529v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference/checkm_data
[2024-01-24 13:41:04,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,565] [INFO] Task started: CheckM
[2024-01-24 13:41:04,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315295.1_ASM331529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315295.1_ASM331529v1_genomic.fna/checkm_input GCF_003315295.1_ASM331529v1_genomic.fna/checkm_result
[2024-01-24 13:41:31,332] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:31,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,365] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:31,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:31,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315295.1_ASM331529v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:31,366] [INFO] Task started: Blastn
[2024-01-24 13:41:31,366] [INFO] Running command: blastn -query GCF_003315295.1_ASM331529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0df8ffce-eb95-4fad-833d-28cd03c837bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315295.1_ASM331529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,205] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,209] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:32,209] [INFO] Target genome list was writen to GCF_003315295.1_ASM331529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:32,220] [INFO] Task started: fastANI
[2024-01-24 13:41:32,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea329a1-bd1e-4ad9-a012-ce52988daba8/GCF_003315295.1_ASM331529v1_genomic.fna.gz --refList GCF_003315295.1_ASM331529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315295.1_ASM331529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:44,083] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,096] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:44,097] [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_003315295.1	s__Paraliobacillus ryukyuensis	100.0	1015	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	conclusive
GCF_001368815.1	s__Paraliobacillus sp001368815	78.6335	282	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	78.2219	270	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110345.1	s__Amphibacillus_D marinus	78.161	73	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908375.1	s__Amphibacillus_C cookii	77.793	111	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	77.7856	193	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900143085.1	s__Gracilibacillus kekensis	77.7826	103	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	77.7643	111	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	77.6038	110	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	77.591	214	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.3128	83	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908325.1	s__Aquibacillus albus	77.223	100	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.165	129	1017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,099] [INFO] GTDB search result was written to GCF_003315295.1_ASM331529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:44,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:44,103] [INFO] DFAST_QC result json was written to GCF_003315295.1_ASM331529v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:44,103] [INFO] DFAST_QC completed!
[2024-01-24 13:41:44,103] [INFO] Total running time: 0h1m1s