[2024-01-25 18:20:20,759] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:20,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:20,760] [INFO] DQC Reference Directory: /var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference
[2024-01-25 18:20:21,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:21,889] [INFO] Task started: Prodigal
[2024-01-25 18:20:21,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6d11315-cfc1-4fdc-9c44-26bd2f80a478/GCF_016909075.1_ASM1690907v1_genomic.fna.gz | prodigal -d GCF_016909075.1_ASM1690907v1_genomic.fna/cds.fna -a GCF_016909075.1_ASM1690907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:29,127] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:29,127] [INFO] Task started: HMMsearch
[2024-01-25 18:20:29,127] [INFO] Running command: hmmsearch --tblout GCF_016909075.1_ASM1690907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference/reference_markers.hmm GCF_016909075.1_ASM1690907v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:29,354] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:29,355] [INFO] Found 6/6 markers.
[2024-01-25 18:20:29,384] [INFO] Query marker FASTA was written to GCF_016909075.1_ASM1690907v1_genomic.fna/markers.fasta
[2024-01-25 18:20:29,385] [INFO] Task started: Blastn
[2024-01-25 18:20:29,385] [INFO] Running command: blastn -query GCF_016909075.1_ASM1690907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference/reference_markers.fasta -out GCF_016909075.1_ASM1690907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:29,954] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:29,958] [INFO] Selected 24 target genomes.
[2024-01-25 18:20:29,958] [INFO] Target genome list was writen to GCF_016909075.1_ASM1690907v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:29,978] [INFO] Task started: fastANI
[2024-01-25 18:20:29,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d11315-cfc1-4fdc-9c44-26bd2f80a478/GCF_016909075.1_ASM1690907v1_genomic.fna.gz --refList GCF_016909075.1_ASM1690907v1_genomic.fna/target_genomes.txt --output GCF_016909075.1_ASM1690907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:46,079] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:46,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:46,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:46,092] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:20:46,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:20:46,092] [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
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	100.0	1311	1311	95	conclusive
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	78.4162	280	1311	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	78.399	280	1311	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_000832985.1	1404	1404	type	True	78.3577	280	1311	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	78.3368	278	1311	95	below_threshold
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	78.1764	290	1311	95	below_threshold
Priestia abyssalis	strain=DSM 25875	GCA_002019595.1	1221450	1221450	type	True	77.4328	207	1311	95	below_threshold
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	77.3854	130	1311	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	77.3608	134	1311	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	77.3568	130	1311	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	77.355	129	1311	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	77.2837	129	1311	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.2774	122	1311	95	below_threshold
Ectobacillus antri	strain=SYSU K30001	GCA_003852715.1	2486280	2486280	type	True	77.2767	83	1311	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	77.2023	138	1311	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	77.1606	126	1311	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	77.0178	78	1311	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.9989	96	1311	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.6741	107	1311	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.4472	66	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:46,094] [INFO] DFAST Taxonomy check result was written to GCF_016909075.1_ASM1690907v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:46,095] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:46,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:46,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference/checkm_data
[2024-01-25 18:20:46,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:46,136] [INFO] Task started: CheckM
[2024-01-25 18:20:46,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909075.1_ASM1690907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909075.1_ASM1690907v1_genomic.fna/checkm_input GCF_016909075.1_ASM1690907v1_genomic.fna/checkm_result
[2024-01-25 18:21:12,538] [INFO] Task succeeded: CheckM
[2024-01-25 18:21:12,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:21:12,559] [INFO] ===== Completeness check finished =====
[2024-01-25 18:21:12,560] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:21:12,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909075.1_ASM1690907v1_genomic.fna/markers.fasta)
[2024-01-25 18:21:12,560] [INFO] Task started: Blastn
[2024-01-25 18:21:12,560] [INFO] Running command: blastn -query GCF_016909075.1_ASM1690907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga297585e-a604-4fe9-91c3-17871942ae07/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909075.1_ASM1690907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:21:13,361] [INFO] Task succeeded: Blastn
[2024-01-25 18:21:13,364] [INFO] Selected 16 target genomes.
[2024-01-25 18:21:13,364] [INFO] Target genome list was writen to GCF_016909075.1_ASM1690907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:21:13,378] [INFO] Task started: fastANI
[2024-01-25 18:21:13,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d11315-cfc1-4fdc-9c44-26bd2f80a478/GCF_016909075.1_ASM1690907v1_genomic.fna.gz --refList GCF_016909075.1_ASM1690907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909075.1_ASM1690907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:27,386] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:27,395] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:21:27,396] [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_016909075.1	s__Priestia iocasae	100.0	1311	1311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003184905.1	s__Priestia sp003184905	82.6671	919	1311	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_008180335.1	s__Priestia megaterium_B	78.5678	323	1311	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_002265635.1	s__Priestia aryabhattai_A	78.4214	295	1311	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_000832985.1	s__Priestia megaterium	78.3624	279	1311	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_009497655.1	s__Priestia megaterium_A	78.2832	279	1311	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_001591565.1	s__Priestia flexa	78.2066	270	1311	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_000956595.1	s__Priestia aryabhattai	78.1764	290	1311	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_001274935.1	s__Bacillus_AG koreensis	77.6782	219	1311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019595.1	s__Bacillus_BA abyssalis	77.4328	207	1311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_BA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383235.1	s__Bacillus_A sp000383235	77.0641	124	1311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	76.6393	92	1311	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_001591645.1	s__Robertmurraya korlensis	76.5294	99	1311	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_005870085.1	s__BH258 sp005870085	76.3173	65	1311	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:21:27,397] [INFO] GTDB search result was written to GCF_016909075.1_ASM1690907v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:27,397] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:27,402] [INFO] DFAST_QC result json was written to GCF_016909075.1_ASM1690907v1_genomic.fna/dqc_result.json
[2024-01-25 18:21:27,402] [INFO] DFAST_QC completed!
[2024-01-25 18:21:27,402] [INFO] Total running time: 0h1m7s