[2024-01-25 18:41:35,781] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:35,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:35,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference
[2024-01-25 18:41:36,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:36,955] [INFO] Task started: Prodigal
[2024-01-25 18:41:36,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgb414daf2-1492-43c9-8166-e8eb4a06483a/GCF_009649745.1_ASM964974v1_genomic.fna.gz | prodigal -d GCF_009649745.1_ASM964974v1_genomic.fna/cds.fna -a GCF_009649745.1_ASM964974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:44,071] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:44,071] [INFO] Task started: HMMsearch
[2024-01-25 18:41:44,071] [INFO] Running command: hmmsearch --tblout GCF_009649745.1_ASM964974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference/reference_markers.hmm GCF_009649745.1_ASM964974v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:44,325] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:44,326] [INFO] Found 6/6 markers.
[2024-01-25 18:41:44,359] [INFO] Query marker FASTA was written to GCF_009649745.1_ASM964974v1_genomic.fna/markers.fasta
[2024-01-25 18:41:44,359] [INFO] Task started: Blastn
[2024-01-25 18:41:44,359] [INFO] Running command: blastn -query GCF_009649745.1_ASM964974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference/reference_markers.fasta -out GCF_009649745.1_ASM964974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:44,908] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:44,913] [INFO] Selected 19 target genomes.
[2024-01-25 18:41:44,914] [INFO] Target genome list was writen to GCF_009649745.1_ASM964974v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:44,919] [INFO] Task started: fastANI
[2024-01-25 18:41:44,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgb414daf2-1492-43c9-8166-e8eb4a06483a/GCF_009649745.1_ASM964974v1_genomic.fna.gz --refList GCF_009649745.1_ASM964974v1_genomic.fna/target_genomes.txt --output GCF_009649745.1_ASM964974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:59,321] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:59,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:59,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:59,330] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:59,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:59,330] [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
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	100.0	1422	1423	95	conclusive
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	79.7395	564	1423	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.6551	204	1423	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.5927	227	1423	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.563	163	1423	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	77.5012	140	1423	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.1885	139	1423	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.1885	118	1423	95	below_threshold
Gracilibacillus dipsosauri	strain=DD1	GCA_003176895.1	178340	178340	type	True	77.143	83	1423	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.9384	111	1423	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.5882	50	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:59,332] [INFO] DFAST Taxonomy check result was written to GCF_009649745.1_ASM964974v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:59,332] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:59,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:59,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference/checkm_data
[2024-01-25 18:41:59,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:59,377] [INFO] Task started: CheckM
[2024-01-25 18:41:59,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649745.1_ASM964974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649745.1_ASM964974v1_genomic.fna/checkm_input GCF_009649745.1_ASM964974v1_genomic.fna/checkm_result
[2024-01-25 18:42:25,221] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:25,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:25,239] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:25,240] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:25,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649745.1_ASM964974v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:25,241] [INFO] Task started: Blastn
[2024-01-25 18:42:25,241] [INFO] Running command: blastn -query GCF_009649745.1_ASM964974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f548f9-b029-4528-8b04-dc75d6460e1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649745.1_ASM964974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:26,023] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:26,026] [INFO] Selected 22 target genomes.
[2024-01-25 18:42:26,026] [INFO] Target genome list was writen to GCF_009649745.1_ASM964974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:26,037] [INFO] Task started: fastANI
[2024-01-25 18:42:26,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgb414daf2-1492-43c9-8166-e8eb4a06483a/GCF_009649745.1_ASM964974v1_genomic.fna.gz --refList GCF_009649745.1_ASM964974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649745.1_ASM964974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:41,448] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:41,457] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:41,458] [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_009649745.1	s__Aquibacillus_A halophilus	100.0	1422	1423	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	conclusive
GCF_014280935.1	s__HU2P27 sp014280935	77.6296	205	1423	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_005870085.1	s__BH258 sp005870085	77.594	208	1423	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_016908325.1	s__Aquibacillus albus	77.5829	227	1423	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_003268595.1	s__Paraliobacillus_A zengyii	77.5644	163	1423	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	77.5241	127	1423	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	77.4874	101	1423	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_007301515.1	s__Radiobacillus deserti	77.3722	134	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	77.3182	55	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	77.218	136	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.1885	118	1423	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_003176895.1	s__Gracilibacillus dipsosauri	77.1248	82	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
GCF_900111445.1	s__Ornithinibacillus limi	76.8302	82	1423	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_009733865.1	s__Oceanobacillus salinisoli	76.7904	85	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:41,459] [INFO] GTDB search result was written to GCF_009649745.1_ASM964974v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:41,460] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:41,462] [INFO] DFAST_QC result json was written to GCF_009649745.1_ASM964974v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:41,463] [INFO] DFAST_QC completed!
[2024-01-25 18:42:41,463] [INFO] Total running time: 0h1m6s