[2024-01-25 18:40:20,927] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:20,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:20,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference
[2024-01-25 18:40:22,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:22,062] [INFO] Task started: Prodigal
[2024-01-25 18:40:22,063] [INFO] Running command: gunzip -c /var/lib/cwl/stga342d287-346c-405e-9a00-1a036ed46c4c/GCF_010614825.1_ASM1061482v1_genomic.fna.gz | prodigal -d GCF_010614825.1_ASM1061482v1_genomic.fna/cds.fna -a GCF_010614825.1_ASM1061482v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:27,750] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:27,750] [INFO] Task started: HMMsearch
[2024-01-25 18:40:27,750] [INFO] Running command: hmmsearch --tblout GCF_010614825.1_ASM1061482v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference/reference_markers.hmm GCF_010614825.1_ASM1061482v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:27,997] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:27,998] [INFO] Found 6/6 markers.
[2024-01-25 18:40:28,024] [INFO] Query marker FASTA was written to GCF_010614825.1_ASM1061482v1_genomic.fna/markers.fasta
[2024-01-25 18:40:28,025] [INFO] Task started: Blastn
[2024-01-25 18:40:28,025] [INFO] Running command: blastn -query GCF_010614825.1_ASM1061482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference/reference_markers.fasta -out GCF_010614825.1_ASM1061482v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:28,586] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:28,589] [INFO] Selected 21 target genomes.
[2024-01-25 18:40:28,590] [INFO] Target genome list was writen to GCF_010614825.1_ASM1061482v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:28,596] [INFO] Task started: fastANI
[2024-01-25 18:40:28,597] [INFO] Running command: fastANI --query /var/lib/cwl/stga342d287-346c-405e-9a00-1a036ed46c4c/GCF_010614825.1_ASM1061482v1_genomic.fna.gz --refList GCF_010614825.1_ASM1061482v1_genomic.fna/target_genomes.txt --output GCF_010614825.1_ASM1061482v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:46,069] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:46,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:46,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:46,081] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:40:46,081] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:40:46,081] [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
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	100.0	1017	1023	95	inconclusive
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	95.4268	927	1023	95	inconclusive
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.2419	324	1023	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.2239	238	1023	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	78.0137	274	1023	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.996	291	1023	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.9337	301	1023	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.7421	260	1023	95	below_threshold
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	77.6714	54	1023	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.667	228	1023	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.6474	313	1023	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.5846	298	1023	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.9503	96	1023	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.9462	145	1023	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.7788	56	1023	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.5215	87	1023	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.3447	97	1023	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.2706	82	1023	95	below_threshold
Schinkia azotoformans	strain=LMG 9581	GCA_000307855.1	1454	1454	type	True	76.0384	66	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:46,083] [INFO] DFAST Taxonomy check result was written to GCF_010614825.1_ASM1061482v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:46,083] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:46,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:46,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference/checkm_data
[2024-01-25 18:40:46,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:46,118] [INFO] Task started: CheckM
[2024-01-25 18:40:46,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010614825.1_ASM1061482v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010614825.1_ASM1061482v1_genomic.fna/checkm_input GCF_010614825.1_ASM1061482v1_genomic.fna/checkm_result
[2024-01-25 18:41:08,918] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:08,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:08,936] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:08,936] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:08,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010614825.1_ASM1061482v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:08,936] [INFO] Task started: Blastn
[2024-01-25 18:41:08,937] [INFO] Running command: blastn -query GCF_010614825.1_ASM1061482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00903d0b-8aa2-41b9-85a0-784d6138c0cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_010614825.1_ASM1061482v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:09,701] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:09,704] [INFO] Selected 25 target genomes.
[2024-01-25 18:41:09,704] [INFO] Target genome list was writen to GCF_010614825.1_ASM1061482v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:09,726] [INFO] Task started: fastANI
[2024-01-25 18:41:09,726] [INFO] Running command: fastANI --query /var/lib/cwl/stga342d287-346c-405e-9a00-1a036ed46c4c/GCF_010614825.1_ASM1061482v1_genomic.fna.gz --refList GCF_010614825.1_ASM1061482v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010614825.1_ASM1061482v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:31,956] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:31,969] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:31,970] [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_010975035.1	s__Neobacillus thermocopriae	95.4131	928	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	conclusive
GCF_016908975.1	s__Neobacillus cucumis	78.2202	236	1023	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_001510715.1	s__Neobacillus sp001510715	78.1762	302	1023	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_018613415.1	s__Neobacillus sp018613415	78.0709	252	1023	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_005154805.1	s__Neobacillus sp005154805	78.036	305	1023	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_001866655.1	s__Neobacillus sp001866655	78.03	248	1023	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_013248975.1	s__Neobacillus endophyticus	78.0001	273	1023	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_900177675.1	s__Neobacillus sp900177675	77.921	293	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCA_000752035.1	s__Neobacillus rubiinfantis	77.8775	230	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002567005.1	s__Neobacillus sp002567005	77.8572	279	1023	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_011250555.1	s__Neobacillus sp011250555	77.8158	285	1023	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	-
GCF_002585305.1	s__Neobacillus sp002585305	77.778	291	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_009928415.1	s__Neobacillus sp009928415	77.7641	257	1023	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_013409995.1	s__Neobacillus niacini_B	77.7289	234	1023	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_000686805.1	s__Neobacillus sp000686805	77.7177	301	1023	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_007678255.1	s__Neobacillus sp007678255	77.6957	295	1023	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_001591485.1	s__Neobacillus fumarioli	77.6535	229	1023	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_013396335.1	s__Neobacillus sp013396335	77.6249	245	1023	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	-
GCA_019219025.1	s__Neobacillus sp019219025	77.5705	305	1023	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_001634285.1	s__Anoxybacillus_A amylolyticus	77.5378	52	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002559145.1	s__Neobacillus sp002559145	77.4999	283	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.43	95.43	0.81	0.81	2	-
GCF_003989135.1	s__Peribacillus cavernae	76.4437	69	1023	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_000307855.1	s__Calidifontibacillus azotoformans	76.0585	65	1023	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	97.05	97.05	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:31,971] [INFO] GTDB search result was written to GCF_010614825.1_ASM1061482v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:31,971] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:31,976] [INFO] DFAST_QC result json was written to GCF_010614825.1_ASM1061482v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:31,976] [INFO] DFAST_QC completed!
[2024-01-25 18:41:31,976] [INFO] Total running time: 0h1m11s