[2024-01-24 12:44:43,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference
[2024-01-24 12:44:45,272] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,273] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,274] [INFO] Running command: gunzip -c /var/lib/cwl/stga9daee52-ab86-47e1-aa79-977cb72b9ce4/GCF_900199725.1_PRJEB21891_genomic.fna.gz | prodigal -d GCF_900199725.1_PRJEB21891_genomic.fna/cds.fna -a GCF_900199725.1_PRJEB21891_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:56,563] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:56,563] [INFO] Task started: HMMsearch
[2024-01-24 12:44:56,563] [INFO] Running command: hmmsearch --tblout GCF_900199725.1_PRJEB21891_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference/reference_markers.hmm GCF_900199725.1_PRJEB21891_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:56,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:56,974] [INFO] Found 6/6 markers.
[2024-01-24 12:44:57,017] [INFO] Query marker FASTA was written to GCF_900199725.1_PRJEB21891_genomic.fna/markers.fasta
[2024-01-24 12:44:57,018] [INFO] Task started: Blastn
[2024-01-24 12:44:57,018] [INFO] Running command: blastn -query GCF_900199725.1_PRJEB21891_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference/reference_markers.fasta -out GCF_900199725.1_PRJEB21891_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:57,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:57,655] [INFO] Selected 20 target genomes.
[2024-01-24 12:44:57,656] [INFO] Target genome list was writen to GCF_900199725.1_PRJEB21891_genomic.fna/target_genomes.txt
[2024-01-24 12:44:57,667] [INFO] Task started: fastANI
[2024-01-24 12:44:57,667] [INFO] Running command: fastANI --query /var/lib/cwl/stga9daee52-ab86-47e1-aa79-977cb72b9ce4/GCF_900199725.1_PRJEB21891_genomic.fna.gz --refList GCF_900199725.1_PRJEB21891_genomic.fna/target_genomes.txt --output GCF_900199725.1_PRJEB21891_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:18,779] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:18,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:18,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:18,795] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:18,795] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:18,796] [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
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	88.6591	1298	1739	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	87.1396	1270	1739	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	80.1936	678	1739	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	79.1812	517	1739	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	78.3578	107	1739	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	78.0781	432	1739	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.9899	206	1739	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	77.8953	260	1739	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.7972	192	1739	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.7944	190	1739	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.7312	193	1739	95	below_threshold
Bacillus oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	77.3493	100	1739	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	77.2452	189	1739	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.159	180	1739	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.88	168	1739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,799] [INFO] DFAST Taxonomy check result was written to GCF_900199725.1_PRJEB21891_genomic.fna/tc_result.tsv
[2024-01-24 12:45:18,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:18,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:18,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference/checkm_data
[2024-01-24 12:45:18,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:18,858] [INFO] Task started: CheckM
[2024-01-24 12:45:18,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199725.1_PRJEB21891_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199725.1_PRJEB21891_genomic.fna/checkm_input GCF_900199725.1_PRJEB21891_genomic.fna/checkm_result
[2024-01-24 12:45:55,859] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:55,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:55,884] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:55,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:55,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199725.1_PRJEB21891_genomic.fna/markers.fasta)
[2024-01-24 12:45:55,885] [INFO] Task started: Blastn
[2024-01-24 12:45:55,885] [INFO] Running command: blastn -query GCF_900199725.1_PRJEB21891_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbec44a-fafe-494c-b16c-1975d666679a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199725.1_PRJEB21891_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:56,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:56,654] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:56,655] [INFO] Target genome list was writen to GCF_900199725.1_PRJEB21891_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:56,671] [INFO] Task started: fastANI
[2024-01-24 12:45:56,671] [INFO] Running command: fastANI --query /var/lib/cwl/stga9daee52-ab86-47e1-aa79-977cb72b9ce4/GCF_900199725.1_PRJEB21891_genomic.fna.gz --refList GCF_900199725.1_PRJEB21891_genomic.fna/target_genomes_gtdb.txt --output GCF_900199725.1_PRJEB21891_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:13,385] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:13,403] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:13,403] [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_900199725.1	s__Cytobacillus massiliigabonensis	99.996	1715	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001420595.1	s__Cytobacillus solani	88.678	1299	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_001439605.1	s__Cytobacillus praedii	87.1453	1270	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_017874625.1	s__Cytobacillus eiseniae	80.2012	677	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	79.2199	514	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	78.9832	310	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_018343665.1	s__Cytobacillus sp018343665	78.9311	527	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039215.1	s__Cytobacillus sp019039215	78.71	437	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509555.1	s__Cytobacillus sp001509555	78.653	408	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182355.1	s__Cytobacillus oceanisediminis_A	78.1489	291	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	78.0881	301	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923245.1	s__Cytobacillus depressus	78.0826	434	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366035.1	s__Cytobacillus oceanisediminis_C	78.036	316	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011250555.1	s__Neobacillus sp011250555	77.3139	200	1739	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:13,405] [INFO] GTDB search result was written to GCF_900199725.1_PRJEB21891_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:13,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:13,409] [INFO] DFAST_QC result json was written to GCF_900199725.1_PRJEB21891_genomic.fna/dqc_result.json
[2024-01-24 12:46:13,409] [INFO] DFAST_QC completed!
[2024-01-24 12:46:13,409] [INFO] Total running time: 0h1m29s