[2024-01-25 18:43:05,923] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:05,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:05,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference
[2024-01-25 18:43:07,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:07,061] [INFO] Task started: Prodigal
[2024-01-25 18:43:07,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa85ee35-9a1f-4bd5-9424-be112c552c3a/GCF_003426025.1_ASM342602v1_genomic.fna.gz | prodigal -d GCF_003426025.1_ASM342602v1_genomic.fna/cds.fna -a GCF_003426025.1_ASM342602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:12,452] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:12,452] [INFO] Task started: HMMsearch
[2024-01-25 18:43:12,452] [INFO] Running command: hmmsearch --tblout GCF_003426025.1_ASM342602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference/reference_markers.hmm GCF_003426025.1_ASM342602v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:12,801] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:12,802] [INFO] Found 6/6 markers.
[2024-01-25 18:43:12,826] [INFO] Query marker FASTA was written to GCF_003426025.1_ASM342602v1_genomic.fna/markers.fasta
[2024-01-25 18:43:12,826] [INFO] Task started: Blastn
[2024-01-25 18:43:12,826] [INFO] Running command: blastn -query GCF_003426025.1_ASM342602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference/reference_markers.fasta -out GCF_003426025.1_ASM342602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:13,382] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:13,385] [INFO] Selected 19 target genomes.
[2024-01-25 18:43:13,385] [INFO] Target genome list was writen to GCF_003426025.1_ASM342602v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:13,395] [INFO] Task started: fastANI
[2024-01-25 18:43:13,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa85ee35-9a1f-4bd5-9424-be112c552c3a/GCF_003426025.1_ASM342602v1_genomic.fna.gz --refList GCF_003426025.1_ASM342602v1_genomic.fna/target_genomes.txt --output GCF_003426025.1_ASM342602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:27,362] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:27,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:27,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:27,370] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:43:27,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:27,370] [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 quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	100.0	1058	1060	95	conclusive
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	99.994	1052	1060	95	conclusive
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	78.6432	404	1060	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	78.5185	320	1060	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	78.1229	193	1060	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.6844	182	1060	95	below_threshold
Pelagirhabdus alkalitolerans	strain=S5	GCA_900096905.1	1612202	1612202	type	True	77.3903	99	1060	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	76.9113	66	1060	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.8382	99	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:27,371] [INFO] DFAST Taxonomy check result was written to GCF_003426025.1_ASM342602v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:27,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:27,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:27,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference/checkm_data
[2024-01-25 18:43:27,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:27,409] [INFO] Task started: CheckM
[2024-01-25 18:43:27,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003426025.1_ASM342602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003426025.1_ASM342602v1_genomic.fna/checkm_input GCF_003426025.1_ASM342602v1_genomic.fna/checkm_result
[2024-01-25 18:43:48,740] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:48,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:48,764] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:48,764] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:48,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003426025.1_ASM342602v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:48,765] [INFO] Task started: Blastn
[2024-01-25 18:43:48,765] [INFO] Running command: blastn -query GCF_003426025.1_ASM342602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg764269ce-9a6f-4656-8a4a-d9669fe0abb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003426025.1_ASM342602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:49,556] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:49,559] [INFO] Selected 20 target genomes.
[2024-01-25 18:43:49,559] [INFO] Target genome list was writen to GCF_003426025.1_ASM342602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:49,571] [INFO] Task started: fastANI
[2024-01-25 18:43:49,571] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa85ee35-9a1f-4bd5-9424-be112c552c3a/GCF_003426025.1_ASM342602v1_genomic.fna.gz --refList GCF_003426025.1_ASM342602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003426025.1_ASM342602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:03,300] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:03,308] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:03,308] [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_003426025.1	s__Paraliobacillus_A quinghaiensis	100.0	1058	1060	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	conclusive
GCF_003268595.1	s__Paraliobacillus_A zengyii	78.6434	407	1060	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_001368815.1	s__Paraliobacillus sp001368815	78.2413	248	1060	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	78.1168	194	1060	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_009649745.1	s__Aquibacillus_A halophilus	77.6878	136	1060	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_003315295.1	s__Paraliobacillus ryukyuensis	77.6844	182	1060	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	77.4194	98	1060	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_016908375.1	s__Amphibacillus_C cookii	77.1163	106	1060	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_018919165.1	s__Amphibacillus sp018919165	76.6925	86	1060	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	76.6901	55	1060	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	76.5543	53	1060	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_014207435.1	s__Salirhabdus euzebyi	76.2514	71	1060	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:03,310] [INFO] GTDB search result was written to GCF_003426025.1_ASM342602v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:03,310] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:03,315] [INFO] DFAST_QC result json was written to GCF_003426025.1_ASM342602v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:03,315] [INFO] DFAST_QC completed!
[2024-01-25 18:44:03,315] [INFO] Total running time: 0h0m57s