[2024-01-24 13:25:29,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference
[2024-01-24 13:25:31,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,246] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,246] [INFO] Running command: gunzip -c /var/lib/cwl/stg933c89c2-6f16-49b3-b5f4-db01d55b47ba/GCF_000832985.1_ASM83298v1_genomic.fna.gz | prodigal -d GCF_000832985.1_ASM83298v1_genomic.fna/cds.fna -a GCF_000832985.1_ASM83298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,857] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,857] [INFO] Running command: hmmsearch --tblout GCF_000832985.1_ASM83298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference/reference_markers.hmm GCF_000832985.1_ASM83298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:43,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:43,242] [INFO] Found 6/6 markers.
[2024-01-24 13:25:43,295] [INFO] Query marker FASTA was written to GCF_000832985.1_ASM83298v1_genomic.fna/markers.fasta
[2024-01-24 13:25:43,295] [INFO] Task started: Blastn
[2024-01-24 13:25:43,295] [INFO] Running command: blastn -query GCF_000832985.1_ASM83298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference/reference_markers.fasta -out GCF_000832985.1_ASM83298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:43,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:43,940] [INFO] Selected 15 target genomes.
[2024-01-24 13:25:43,941] [INFO] Target genome list was writen to GCF_000832985.1_ASM83298v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:43,951] [INFO] Task started: fastANI
[2024-01-24 13:25:43,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg933c89c2-6f16-49b3-b5f4-db01d55b47ba/GCF_000832985.1_ASM83298v1_genomic.fna.gz --refList GCF_000832985.1_ASM83298v1_genomic.fna/target_genomes.txt --output GCF_000832985.1_ASM83298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:01,685] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:01,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:01,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:01,698] [INFO] Found 15 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 13:26:01,699] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:26:01,699] [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
Priestia megaterium	strain=ATCC 14581	GCA_000832985.1	1404	1404	type	True	100.0	1911	1912	95	inconclusive
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	99.9985	1902	1912	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	99.9951	1904	1912	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_017086525.1	1404	1404	type	True	99.9944	1907	1912	95	inconclusive
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	99.9884	1812	1912	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	97.822	1633	1912	95	inconclusive
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	95.3298	1530	1912	95	inconclusive
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	79.7769	83	1912	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	78.5114	271	1912	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	78.3704	68	1912	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	77.1908	110	1912	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.0982	99	1912	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.7947	119	1912	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.7142	71	1912	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.3498	100	1912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,701] [INFO] DFAST Taxonomy check result was written to GCF_000832985.1_ASM83298v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:01,701] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:01,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:01,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference/checkm_data
[2024-01-24 13:26:01,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:01,760] [INFO] Task started: CheckM
[2024-01-24 13:26:01,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000832985.1_ASM83298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000832985.1_ASM83298v1_genomic.fna/checkm_input GCF_000832985.1_ASM83298v1_genomic.fna/checkm_result
[2024-01-24 13:26:41,180] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:41,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:41,208] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:41,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:41,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000832985.1_ASM83298v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:41,210] [INFO] Task started: Blastn
[2024-01-24 13:26:41,210] [INFO] Running command: blastn -query GCF_000832985.1_ASM83298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46b1f63d-8eb3-42ab-a6df-f6e234557d35/dqc_reference/reference_markers_gtdb.fasta -out GCF_000832985.1_ASM83298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:42,009] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:42,018] [INFO] Selected 11 target genomes.
[2024-01-24 13:26:42,019] [INFO] Target genome list was writen to GCF_000832985.1_ASM83298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:42,032] [INFO] Task started: fastANI
[2024-01-24 13:26:42,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg933c89c2-6f16-49b3-b5f4-db01d55b47ba/GCF_000832985.1_ASM83298v1_genomic.fna.gz --refList GCF_000832985.1_ASM83298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000832985.1_ASM83298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:52,753] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:52,770] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:52,771] [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_000832985.1	s__Priestia megaterium	100.0	1911	1912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	conclusive
GCF_000956595.1	s__Priestia aryabhattai	95.3433	1529	1912	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_009497655.1	s__Priestia megaterium_A	95.1926	1547	1912	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_008180335.1	s__Priestia megaterium_B	79.8262	517	1912	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_001591565.1	s__Priestia flexa	79.6609	416	1912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_002265635.1	s__Priestia aryabhattai_A	79.4728	453	1912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	98.53	98.16	0.94	0.93	4	-
GCF_016909075.1	s__Priestia iocasae	78.4968	272	1912	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_900116295.1	s__Bacillus_A sp900116295	76.9699	146	1912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001509555.1	s__Cytobacillus sp001509555	76.9624	92	1912	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_001591585.1	s__Niallia circulans	76.8702	97	1912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
GCF_003570725.1	s__Peribacillus asahii	76.7887	135	1912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,772] [INFO] GTDB search result was written to GCF_000832985.1_ASM83298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:52,773] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:52,777] [INFO] DFAST_QC result json was written to GCF_000832985.1_ASM83298v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:52,777] [INFO] DFAST_QC completed!
[2024-01-24 13:26:52,778] [INFO] Total running time: 0h1m23s