[2024-01-24 13:56:13,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,011] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,011] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference
[2024-01-24 13:56:14,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,423] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg31ab6094-5811-4e49-9a71-dcc55714ff10/GCF_015482585.1_ASM1548258v1_genomic.fna.gz | prodigal -d GCF_015482585.1_ASM1548258v1_genomic.fna/cds.fna -a GCF_015482585.1_ASM1548258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:20,899] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:20,900] [INFO] Task started: HMMsearch
[2024-01-24 13:56:20,900] [INFO] Running command: hmmsearch --tblout GCF_015482585.1_ASM1548258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference/reference_markers.hmm GCF_015482585.1_ASM1548258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:21,182] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:21,183] [INFO] Found 6/6 markers.
[2024-01-24 13:56:21,213] [INFO] Query marker FASTA was written to GCF_015482585.1_ASM1548258v1_genomic.fna/markers.fasta
[2024-01-24 13:56:21,214] [INFO] Task started: Blastn
[2024-01-24 13:56:21,214] [INFO] Running command: blastn -query GCF_015482585.1_ASM1548258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference/reference_markers.fasta -out GCF_015482585.1_ASM1548258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:21,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:21,861] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:21,861] [INFO] Target genome list was writen to GCF_015482585.1_ASM1548258v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:21,886] [INFO] Task started: fastANI
[2024-01-24 13:56:21,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ab6094-5811-4e49-9a71-dcc55714ff10/GCF_015482585.1_ASM1548258v1_genomic.fna.gz --refList GCF_015482585.1_ASM1548258v1_genomic.fna/target_genomes.txt --output GCF_015482585.1_ASM1548258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:37,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:37,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:37,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:37,332] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:37,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:37,332] [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
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	100.0	1048	1050	95	conclusive
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	81.8593	56	1050	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.8696	110	1050	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	79.8542	97	1050	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	79.5761	98	1050	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	77.18	72	1050	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	77.0877	86	1050	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	77.0014	92	1050	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.9335	76	1050	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	76.9244	74	1050	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.8839	78	1050	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.8104	70	1050	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.4234	62	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,335] [INFO] DFAST Taxonomy check result was written to GCF_015482585.1_ASM1548258v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:37,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:37,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:37,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference/checkm_data
[2024-01-24 13:56:37,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:37,371] [INFO] Task started: CheckM
[2024-01-24 13:56:37,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015482585.1_ASM1548258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015482585.1_ASM1548258v1_genomic.fna/checkm_input GCF_015482585.1_ASM1548258v1_genomic.fna/checkm_result
[2024-01-24 13:57:03,627] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:03,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:03,651] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:03,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:03,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015482585.1_ASM1548258v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:03,653] [INFO] Task started: Blastn
[2024-01-24 13:57:03,653] [INFO] Running command: blastn -query GCF_015482585.1_ASM1548258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4efee4f-396a-465d-a33a-34cb8f9aaa96/dqc_reference/reference_markers_gtdb.fasta -out GCF_015482585.1_ASM1548258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:04,461] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:04,464] [INFO] Selected 26 target genomes.
[2024-01-24 13:57:04,465] [INFO] Target genome list was writen to GCF_015482585.1_ASM1548258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:04,485] [INFO] Task started: fastANI
[2024-01-24 13:57:04,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ab6094-5811-4e49-9a71-dcc55714ff10/GCF_015482585.1_ASM1548258v1_genomic.fna.gz --refList GCF_015482585.1_ASM1548258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015482585.1_ASM1548258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:26,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:26,265] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:26,265] [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
GCA_015482585.1	s__R1DC41 sp015482585	100.0	1050	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__R1DC41;g__R1DC41	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900240995.1	s__OESV01 sp900240995	80.2767	59	1050	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_000832985.1	s__Priestia megaterium	80.2573	90	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	-
GCF_000832605.1	s__Bacillus_A mycoides	79.7613	95	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.01	96.59	0.88	0.83	125	-
GCF_003586445.1	s__Robertmurraya sp003586445	79.5064	97	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002276165.1	s__Cytobacillus kochii	79.4358	81	1050	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_014960805.1	s__Bacillus_BV sp014960805	79.424	81	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018742245.1	s__Bacillus_A cereus_U	79.4076	104	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.53	95.81	0.88	0.84	34	-
GCF_009497655.1	s__Priestia megaterium_A	79.3756	77	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	98.08	96.36	0.92	0.89	34	-
GCF_000291355.1	s__Bacillus_A cereus_O	78.8171	92	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.56	96.56	0.88	0.83	4	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	78.7637	85	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837155.1	s__Litchfieldia sp014837155	77.4268	80	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908835.1	s__Bacillus_AD endoradicis	77.3134	77	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590835.1	s__Bacillus_A gaemokensis	77.18	72	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000956595.1	s__Priestia aryabhattai	77.0454	70	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	96.022	97.07	96.58	0.92	0.91	12	-
GCF_009928415.1	s__Neobacillus sp009928415	77.0324	57	1050	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_000380245.2	s__Bacillus_AD massiliogorillae	77.0293	91	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	77.0247	73	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006546985.1	s__VATK01 sp006546985	76.8715	50	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__VATK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908495.1	s__Bacillus_BW pakistanensis	76.8549	79	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BW	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002567495.1	s__Bacillus_A cereus_AQ	76.72	82	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.10	96.80	0.92	0.88	3	-
GCF_014836495.1	s__Cytobacillus sp014836495	76.6139	64	1050	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_007679095.1	s__DE0126 sp007679095	76.5221	52	1050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:26,267] [INFO] GTDB search result was written to GCF_015482585.1_ASM1548258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:26,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:26,276] [INFO] DFAST_QC result json was written to GCF_015482585.1_ASM1548258v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:26,276] [INFO] DFAST_QC completed!
[2024-01-24 13:57:26,276] [INFO] Total running time: 0h1m13s