[2024-01-24 13:22:31,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference
[2024-01-24 13:22:32,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,586] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,587] [INFO] Running command: gunzip -c /var/lib/cwl/stg60760dbc-53c0-49bc-a489-79fcf572dd51/GCF_017086525.1_ASM1708652v1_genomic.fna.gz | prodigal -d GCF_017086525.1_ASM1708652v1_genomic.fna/cds.fna -a GCF_017086525.1_ASM1708652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:44,063] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:44,064] [INFO] Task started: HMMsearch
[2024-01-24 13:22:44,064] [INFO] Running command: hmmsearch --tblout GCF_017086525.1_ASM1708652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference/reference_markers.hmm GCF_017086525.1_ASM1708652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:44,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:44,387] [INFO] Found 6/6 markers.
[2024-01-24 13:22:44,439] [INFO] Query marker FASTA was written to GCF_017086525.1_ASM1708652v1_genomic.fna/markers.fasta
[2024-01-24 13:22:44,439] [INFO] Task started: Blastn
[2024-01-24 13:22:44,439] [INFO] Running command: blastn -query GCF_017086525.1_ASM1708652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference/reference_markers.fasta -out GCF_017086525.1_ASM1708652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:45,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:45,059] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:45,059] [INFO] Target genome list was writen to GCF_017086525.1_ASM1708652v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:45,060] [INFO] Task started: fastANI
[2024-01-24 13:22:45,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg60760dbc-53c0-49bc-a489-79fcf572dd51/GCF_017086525.1_ASM1708652v1_genomic.fna.gz --refList GCF_017086525.1_ASM1708652v1_genomic.fna/target_genomes.txt --output GCF_017086525.1_ASM1708652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:00,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:00,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:00,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:00,815] [INFO] Found 15 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 13:23:00,816] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:23:00,816] [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_017086525.1	1404	1404	type	True	100.0	1910	1911	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_000832985.1	1404	1404	type	True	99.9968	1901	1911	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	99.9952	1904	1911	95	inconclusive
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	99.9909	1895	1911	95	inconclusive
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	99.9828	1810	1911	95	inconclusive
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	97.8272	1629	1911	95	inconclusive
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	95.3624	1527	1911	95	inconclusive
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	79.289	94	1911	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	78.4766	284	1911	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	77.9404	67	1911	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	77.2663	105	1911	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.1585	94	1911	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.7502	95	1911	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.7329	63	1911	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.7227	120	1911	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:00,818] [INFO] DFAST Taxonomy check result was written to GCF_017086525.1_ASM1708652v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:00,818] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:00,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:00,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference/checkm_data
[2024-01-24 13:23:00,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:00,881] [INFO] Task started: CheckM
[2024-01-24 13:23:00,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017086525.1_ASM1708652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017086525.1_ASM1708652v1_genomic.fna/checkm_input GCF_017086525.1_ASM1708652v1_genomic.fna/checkm_result
[2024-01-24 13:23:39,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:39,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,538] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:39,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:39,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017086525.1_ASM1708652v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:39,539] [INFO] Task started: Blastn
[2024-01-24 13:23:39,539] [INFO] Running command: blastn -query GCF_017086525.1_ASM1708652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff64cb52-272d-4ad5-a5b5-35c510db48fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_017086525.1_ASM1708652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:40,319] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:40,323] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:40,323] [INFO] Target genome list was writen to GCF_017086525.1_ASM1708652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:40,325] [INFO] Task started: fastANI
[2024-01-24 13:23:40,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg60760dbc-53c0-49bc-a489-79fcf572dd51/GCF_017086525.1_ASM1708652v1_genomic.fna.gz --refList GCF_017086525.1_ASM1708652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017086525.1_ASM1708652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:51,173] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:51,191] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:51,191] [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	99.9968	1901	1911	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	95.3734	1526	1911	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	95.1899	1537	1911	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	79.8438	516	1911	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	79.5787	419	1911	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	79.4356	452	1911	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	78.4826	284	1911	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	77.1316	130	1911	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_001591585.1	s__Niallia circulans	76.8644	103	1911	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	76.8497	127	1911	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	-
GCF_001509555.1	s__Cytobacillus sp001509555	76.7921	96	1911	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:51,193] [INFO] GTDB search result was written to GCF_017086525.1_ASM1708652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:51,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:51,198] [INFO] DFAST_QC result json was written to GCF_017086525.1_ASM1708652v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:51,199] [INFO] DFAST_QC completed!
[2024-01-24 13:23:51,199] [INFO] Total running time: 0h1m20s