[2024-01-24 12:37:25,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,124] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference
[2024-01-24 12:37:26,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,503] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,504] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f87acd8-5bab-4cca-86c8-b2e65aaa8bd2/GCF_014196195.1_ASM1419619v1_genomic.fna.gz | prodigal -d GCF_014196195.1_ASM1419619v1_genomic.fna/cds.fna -a GCF_014196195.1_ASM1419619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:35,715] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:35,715] [INFO] Task started: HMMsearch
[2024-01-24 12:37:35,715] [INFO] Running command: hmmsearch --tblout GCF_014196195.1_ASM1419619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference/reference_markers.hmm GCF_014196195.1_ASM1419619v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:36,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:36,019] [INFO] Found 6/6 markers.
[2024-01-24 12:37:36,055] [INFO] Query marker FASTA was written to GCF_014196195.1_ASM1419619v1_genomic.fna/markers.fasta
[2024-01-24 12:37:36,056] [INFO] Task started: Blastn
[2024-01-24 12:37:36,056] [INFO] Running command: blastn -query GCF_014196195.1_ASM1419619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference/reference_markers.fasta -out GCF_014196195.1_ASM1419619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:36,638] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:36,643] [INFO] Selected 29 target genomes.
[2024-01-24 12:37:36,643] [INFO] Target genome list was writen to GCF_014196195.1_ASM1419619v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:36,656] [INFO] Task started: fastANI
[2024-01-24 12:37:36,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f87acd8-5bab-4cca-86c8-b2e65aaa8bd2/GCF_014196195.1_ASM1419619v1_genomic.fna.gz --refList GCF_014196195.1_ASM1419619v1_genomic.fna/target_genomes.txt --output GCF_014196195.1_ASM1419619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:53,159] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:53,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:53,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:53,173] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:53,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:53,173] [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
Anoxybacillus rupiensis	strain=DSM 17127	GCA_014196195.1	311460	311460	type	True	100.0	1217	1219	95	conclusive
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	78.5419	342	1219	95	below_threshold
Anoxybacillus voinovskiensis	strain=JCM 12111	GCA_014646615.1	230470	230470	type	True	78.5408	393	1219	95	below_threshold
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	78.5307	397	1219	95	below_threshold
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	78.5207	380	1219	95	below_threshold
Anoxybacillus caldiproteolyticus	strain=DSM 15730	GCA_013761245.1	247480	247480	type	True	78.5166	412	1219	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_001187595.1	198467	198467	suspected-type	True	78.2762	203	1219	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	77.8999	199	1219	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	77.8321	342	1219	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	77.828	345	1219	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	77.8256	342	1219	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	76.7866	52	1219	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	76.3391	62	1219	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	75.942	66	1219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:53,175] [INFO] DFAST Taxonomy check result was written to GCF_014196195.1_ASM1419619v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:53,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:53,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:53,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference/checkm_data
[2024-01-24 12:37:53,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:53,217] [INFO] Task started: CheckM
[2024-01-24 12:37:53,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196195.1_ASM1419619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196195.1_ASM1419619v1_genomic.fna/checkm_input GCF_014196195.1_ASM1419619v1_genomic.fna/checkm_result
[2024-01-24 12:38:25,509] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:25,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,531] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:25,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:25,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196195.1_ASM1419619v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:25,533] [INFO] Task started: Blastn
[2024-01-24 12:38:25,533] [INFO] Running command: blastn -query GCF_014196195.1_ASM1419619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf1340c0-bc70-475d-9c12-aa3a4af4efbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196195.1_ASM1419619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:26,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:26,315] [INFO] Selected 25 target genomes.
[2024-01-24 12:38:26,315] [INFO] Target genome list was writen to GCF_014196195.1_ASM1419619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:26,337] [INFO] Task started: fastANI
[2024-01-24 12:38:26,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f87acd8-5bab-4cca-86c8-b2e65aaa8bd2/GCF_014196195.1_ASM1419619v1_genomic.fna.gz --refList GCF_014196195.1_ASM1419619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196195.1_ASM1419619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:42,210] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:42,228] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:42,228] [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_014196195.1	s__Anoxybacillus_A rupiensis	100.0	1217	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	98.88	98.54	0.93	0.92	7	conclusive
GCF_000620165.1	s__Anoxybacillus_A tepidamans_A	80.1331	576	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201465.1	s__Anoxybacillus_A tepidamans	79.1835	498	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196205.1	s__Anoxybacillus_A voinovskiensis	78.5307	397	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003259935.1	s__Anoxybacillus_B vitaminiphilus	78.5283	344	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013761245.1	s__Anoxybacillus_C caldiproteolyticus	78.5166	412	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_C	95.0	99.29	99.25	0.94	0.93	3	-
GCF_001634285.1	s__Anoxybacillus_A amylolyticus	78.511	382	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187595.1	s__Anoxybacillus gonensis	78.2753	203	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	77.9872	324	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_003688615.2	s__Parageobacillus toebii	77.8411	346	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	77.7218	320	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111795.1	s__Anoxybacillus pushchinoensis	77.7182	182	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	95.71	95.71	0.84	0.84	2	-
GCF_018283675.1	s__Metabacillus_B sp018283675	76.7866	52	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	76.3391	62	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180335.1	s__Priestia megaterium_B	76.3294	69	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318295.1	s__Maribacillus taeanensis	75.942	66	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981385.1	s__Metabacillus sp000981385	75.7957	54	1219	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:42,229] [INFO] GTDB search result was written to GCF_014196195.1_ASM1419619v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:42,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:42,235] [INFO] DFAST_QC result json was written to GCF_014196195.1_ASM1419619v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:42,235] [INFO] DFAST_QC completed!
[2024-01-24 12:38:42,235] [INFO] Total running time: 0h1m17s