[2024-01-24 13:09:50,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:50,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:50,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference
[2024-01-24 13:09:52,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,050] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,051] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6f74ee0-7c01-4442-a51e-295889f18e42/GCF_000507145.1_KCTC_13622_01_genomic.fna.gz | prodigal -d GCF_000507145.1_KCTC_13622_01_genomic.fna/cds.fna -a GCF_000507145.1_KCTC_13622_01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:02,415] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:02,415] [INFO] Task started: HMMsearch
[2024-01-24 13:10:02,415] [INFO] Running command: hmmsearch --tblout GCF_000507145.1_KCTC_13622_01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference/reference_markers.hmm GCF_000507145.1_KCTC_13622_01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:02,759] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:02,760] [INFO] Found 6/6 markers.
[2024-01-24 13:10:02,796] [INFO] Query marker FASTA was written to GCF_000507145.1_KCTC_13622_01_genomic.fna/markers.fasta
[2024-01-24 13:10:02,796] [INFO] Task started: Blastn
[2024-01-24 13:10:02,797] [INFO] Running command: blastn -query GCF_000507145.1_KCTC_13622_01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference/reference_markers.fasta -out GCF_000507145.1_KCTC_13622_01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:03,460] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:03,463] [INFO] Selected 10 target genomes.
[2024-01-24 13:10:03,464] [INFO] Target genome list was writen to GCF_000507145.1_KCTC_13622_01_genomic.fna/target_genomes.txt
[2024-01-24 13:10:03,478] [INFO] Task started: fastANI
[2024-01-24 13:10:03,479] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f74ee0-7c01-4442-a51e-295889f18e42/GCF_000507145.1_KCTC_13622_01_genomic.fna.gz --refList GCF_000507145.1_KCTC_13622_01_genomic.fna/target_genomes.txt --output GCF_000507145.1_KCTC_13622_01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:12,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:12,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:12,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:12,869] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:12,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:12,869] [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
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	100.0	1305	1307	95	conclusive
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	99.9399	1124	1307	95	conclusive
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	92.3214	1141	1307	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	92.2784	1148	1307	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	92.2203	1124	1307	95	below_threshold
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	92.2121	1143	1307	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	91.3136	1150	1307	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	91.2913	1142	1307	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	90.3468	1003	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:12,871] [INFO] DFAST Taxonomy check result was written to GCF_000507145.1_KCTC_13622_01_genomic.fna/tc_result.tsv
[2024-01-24 13:10:12,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:12,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:12,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference/checkm_data
[2024-01-24 13:10:12,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:12,916] [INFO] Task started: CheckM
[2024-01-24 13:10:12,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000507145.1_KCTC_13622_01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000507145.1_KCTC_13622_01_genomic.fna/checkm_input GCF_000507145.1_KCTC_13622_01_genomic.fna/checkm_result
[2024-01-24 13:10:48,598] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:48,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:48,614] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:48,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:48,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000507145.1_KCTC_13622_01_genomic.fna/markers.fasta)
[2024-01-24 13:10:48,615] [INFO] Task started: Blastn
[2024-01-24 13:10:48,616] [INFO] Running command: blastn -query GCF_000507145.1_KCTC_13622_01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdda00ea9-b003-4d5c-9d47-47f52f332c69/dqc_reference/reference_markers_gtdb.fasta -out GCF_000507145.1_KCTC_13622_01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:49,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:49,368] [INFO] Selected 7 target genomes.
[2024-01-24 13:10:49,368] [INFO] Target genome list was writen to GCF_000507145.1_KCTC_13622_01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:49,373] [INFO] Task started: fastANI
[2024-01-24 13:10:49,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f74ee0-7c01-4442-a51e-295889f18e42/GCF_000507145.1_KCTC_13622_01_genomic.fna.gz --refList GCF_000507145.1_KCTC_13622_01_genomic.fna/target_genomes_gtdb.txt --output GCF_000507145.1_KCTC_13622_01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:56,404] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:56,417] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:56,417] [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_000507145.1	s__Bacillus tequilensis	100.0	1305	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	conclusive
GCF_004124315.1	s__Bacillus cabrialesii	93.2948	1153	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCA_000332645.1	s__Bacillus inaquosorum	92.3214	1141	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_000227465.1	s__Bacillus spizizenii	92.1912	1145	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCF_000009045.1	s__Bacillus subtilis	91.3032	1139	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_002153395.1	s__Bacillus subtilis_G	91.2869	1130	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_010093085.1	s__Bacillus sp010093085	90.4843	1059	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:56,419] [INFO] GTDB search result was written to GCF_000507145.1_KCTC_13622_01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:56,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:56,423] [INFO] DFAST_QC result json was written to GCF_000507145.1_KCTC_13622_01_genomic.fna/dqc_result.json
[2024-01-24 13:10:56,423] [INFO] DFAST_QC completed!
[2024-01-24 13:10:56,423] [INFO] Total running time: 0h1m6s