[2024-01-24 12:06:50,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,711] [INFO] DQC Reference Directory: /var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference
[2024-01-24 12:06:51,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,909] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg18b1b3eb-1103-492a-8749-48857d8a5192/GCF_014083865.1_ASM1408386v1_genomic.fna.gz | prodigal -d GCF_014083865.1_ASM1408386v1_genomic.fna/cds.fna -a GCF_014083865.1_ASM1408386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:57,253] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:57,253] [INFO] Task started: HMMsearch
[2024-01-24 12:06:57,254] [INFO] Running command: hmmsearch --tblout GCF_014083865.1_ASM1408386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference/reference_markers.hmm GCF_014083865.1_ASM1408386v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:57,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:57,509] [INFO] Found 6/6 markers.
[2024-01-24 12:06:57,535] [INFO] Query marker FASTA was written to GCF_014083865.1_ASM1408386v1_genomic.fna/markers.fasta
[2024-01-24 12:06:57,535] [INFO] Task started: Blastn
[2024-01-24 12:06:57,536] [INFO] Running command: blastn -query GCF_014083865.1_ASM1408386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference/reference_markers.fasta -out GCF_014083865.1_ASM1408386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:58,134] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:58,139] [INFO] Selected 22 target genomes.
[2024-01-24 12:06:58,139] [INFO] Target genome list was writen to GCF_014083865.1_ASM1408386v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:58,148] [INFO] Task started: fastANI
[2024-01-24 12:06:58,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b1b3eb-1103-492a-8749-48857d8a5192/GCF_014083865.1_ASM1408386v1_genomic.fna.gz --refList GCF_014083865.1_ASM1408386v1_genomic.fna/target_genomes.txt --output GCF_014083865.1_ASM1408386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:10,345] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:10,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:10,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:10,359] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:10,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:10,359] [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 salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	100.0	916	917	95	conclusive
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	78.3641	252	917	95	below_threshold
Pelagirhabdus alkalitolerans	strain=S5	GCA_900096905.1	1612202	1612202	type	True	78.1594	92	917	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.9198	209	917	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	77.875	210	917	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.6687	99	917	95	below_threshold
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	77.6099	75	917	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	77.2124	118	917	95	below_threshold
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	77.1995	115	917	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.0832	131	917	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	77.0416	156	917	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:10,361] [INFO] DFAST Taxonomy check result was written to GCF_014083865.1_ASM1408386v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:10,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:10,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:10,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference/checkm_data
[2024-01-24 12:07:10,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:10,394] [INFO] Task started: CheckM
[2024-01-24 12:07:10,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014083865.1_ASM1408386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014083865.1_ASM1408386v1_genomic.fna/checkm_input GCF_014083865.1_ASM1408386v1_genomic.fna/checkm_result
[2024-01-24 12:07:33,155] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:33,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,177] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:33,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:33,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014083865.1_ASM1408386v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:33,178] [INFO] Task started: Blastn
[2024-01-24 12:07:33,178] [INFO] Running command: blastn -query GCF_014083865.1_ASM1408386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf807ca9f-74e9-49ca-a501-008da1a239e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014083865.1_ASM1408386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:34,030] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:34,033] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:34,033] [INFO] Target genome list was writen to GCF_014083865.1_ASM1408386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:34,046] [INFO] Task started: fastANI
[2024-01-24 12:07:34,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b1b3eb-1103-492a-8749-48857d8a5192/GCF_014083865.1_ASM1408386v1_genomic.fna.gz --refList GCF_014083865.1_ASM1408386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014083865.1_ASM1408386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:44,585] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:44,599] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:44,600] [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_014083865.1	s__Paraliobacillus salinarum	100.0	916	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001368815.1	s__Paraliobacillus sp001368815	80.9044	578	917	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_003315295.1	s__Paraliobacillus ryukyuensis	78.3641	252	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_900096905.1	s__Pelagirhabdus alkalitolerans	78.1594	92	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pelagirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	77.8737	210	917	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_016908325.1	s__Aquibacillus albus	77.6448	101	917	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_016908375.1	s__Amphibacillus_C cookii	77.6315	103	917	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	77.6289	195	917	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_009498735.1	s__Gracilibacillus sp009498735	77.5789	74	917	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_003337485.1	s__Saliterribacillus persicus	77.2699	119	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649745.1	s__Aquibacillus_A halophilus	77.1995	115	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.0813	131	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111445.1	s__Ornithinibacillus limi	76.7785	76	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,601] [INFO] GTDB search result was written to GCF_014083865.1_ASM1408386v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:44,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:44,605] [INFO] DFAST_QC result json was written to GCF_014083865.1_ASM1408386v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:44,605] [INFO] DFAST_QC completed!
[2024-01-24 12:07:44,605] [INFO] Total running time: 0h0m54s