[2024-01-25 19:56:05,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:05,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:05,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference
[2024-01-25 19:56:06,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:06,936] [INFO] Task started: Prodigal
[2024-01-25 19:56:06,937] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4e491aa-f531-45dc-93e1-df0ac23ae557/GCF_030813365.1_ASM3081336v1_genomic.fna.gz | prodigal -d GCF_030813365.1_ASM3081336v1_genomic.fna/cds.fna -a GCF_030813365.1_ASM3081336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:12,768] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:12,768] [INFO] Task started: HMMsearch
[2024-01-25 19:56:12,768] [INFO] Running command: hmmsearch --tblout GCF_030813365.1_ASM3081336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference/reference_markers.hmm GCF_030813365.1_ASM3081336v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:12,993] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:12,995] [INFO] Found 6/6 markers.
[2024-01-25 19:56:13,023] [INFO] Query marker FASTA was written to GCF_030813365.1_ASM3081336v1_genomic.fna/markers.fasta
[2024-01-25 19:56:13,023] [INFO] Task started: Blastn
[2024-01-25 19:56:13,024] [INFO] Running command: blastn -query GCF_030813365.1_ASM3081336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference/reference_markers.fasta -out GCF_030813365.1_ASM3081336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:13,572] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:13,575] [INFO] Selected 34 target genomes.
[2024-01-25 19:56:13,575] [INFO] Target genome list was writen to GCF_030813365.1_ASM3081336v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:13,597] [INFO] Task started: fastANI
[2024-01-25 19:56:13,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e491aa-f531-45dc-93e1-df0ac23ae557/GCF_030813365.1_ASM3081336v1_genomic.fna.gz --refList GCF_030813365.1_ASM3081336v1_genomic.fna/target_genomes.txt --output GCF_030813365.1_ASM3081336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:35,968] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:35,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:35,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:35,985] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:56:35,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:56:35,985] [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
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.6323	101	1072	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	77.4642	82	1072	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	77.4613	75	1072	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	77.3272	60	1072	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	77.2214	124	1072	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	77.0947	68	1072	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_001315165.1	308892	308892	type	True	77.0635	58	1072	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_000517385.1	308892	308892	type	True	77.018	58	1072	95	below_threshold
Bacillus wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	76.9787	97	1072	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.9769	69	1072	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.9085	109	1072	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	76.8893	75	1072	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.8591	79	1072	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.8408	70	1072	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	76.8352	84	1072	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	76.8189	91	1072	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	76.7552	91	1072	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	76.7157	75	1072	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	76.6985	64	1072	95	below_threshold
Bacillus smithii	strain=NBRC 15311	GCA_001591985.1	1479	1479	type	True	76.6925	78	1072	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	76.6549	70	1072	95	below_threshold
Bacillus smithii	strain=DSM 4216	GCA_001050115.1	1479	1479	type	True	76.6144	81	1072	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.6061	67	1072	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.5908	110	1072	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	76.5632	89	1072	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	76.524	77	1072	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.4442	80	1072	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.3416	85	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:35,987] [INFO] DFAST Taxonomy check result was written to GCF_030813365.1_ASM3081336v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:35,987] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:35,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:35,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference/checkm_data
[2024-01-25 19:56:35,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:36,024] [INFO] Task started: CheckM
[2024-01-25 19:56:36,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813365.1_ASM3081336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813365.1_ASM3081336v1_genomic.fna/checkm_input GCF_030813365.1_ASM3081336v1_genomic.fna/checkm_result
[2024-01-25 19:56:58,655] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:58,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:58,673] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:58,674] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:58,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813365.1_ASM3081336v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:58,674] [INFO] Task started: Blastn
[2024-01-25 19:56:58,674] [INFO] Running command: blastn -query GCF_030813365.1_ASM3081336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5792cc03-a560-471d-a693-f202e6747e81/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813365.1_ASM3081336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:59,434] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:59,437] [INFO] Selected 34 target genomes.
[2024-01-25 19:56:59,438] [INFO] Target genome list was writen to GCF_030813365.1_ASM3081336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:59,480] [INFO] Task started: fastANI
[2024-01-25 19:56:59,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e491aa-f531-45dc-93e1-df0ac23ae557/GCF_030813365.1_ASM3081336v1_genomic.fna.gz --refList GCF_030813365.1_ASM3081336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813365.1_ASM3081336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:24,814] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:24,832] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:57:24,832] [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_003667865.1	s__Bacillus_BQ marisflavi_A	77.7428	82	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008764245.1	s__Lederbergia ruris	77.6368	67	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	98.48	98.48	0.86	0.86	2	-
GCF_001076885.1	s__Niallia sp001076885	77.6091	96	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.59	99.45	0.92	0.91	4	-
GCF_001274935.1	s__Bacillus_AG koreensis	77.416	73	1072	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	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	77.3524	114	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002261155.1	s__FJAT-46582 sp002261155	77.2252	124	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772275.1	s__Heyndrickxia vini	77.1669	124	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820555.1	s__FJAT-46582 sp016820555	77.1305	128	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180865.1	s__Rossellomorea aquimaris_D	77.0933	86	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	97.97	97.96	0.89	0.89	3	-
GCF_007679095.1	s__DE0126 sp007679095	77.0825	85	1072	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	-
GCF_009497655.1	s__Priestia megaterium_A	77.0444	70	1072	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_003600835.1	s__Pseudobacillus sp003600835	77.007	91	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	76.9792	69	1072	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_004006295.1	s__Peribacillus asahii_A	76.9427	111	1072	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	-
GCA_900199695.1	s__Niallia sp900199695	76.9148	95	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	98.49	98.15	0.84	0.82	5	-
GCF_001420595.1	s__Cytobacillus solani	76.9085	109	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_012843265.1	s__Bacillus_BU sp012843265	76.8988	78	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115925.1	s__CL95 sp900115925	76.8751	84	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__CL95	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003668575.1	s__Falsibacillus albus	76.8591	79	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	76.8408	70	1072	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_001648555.1	s__Rossellomorea aquimaris	76.8189	91	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814275.1	s__Gottfriedia sp017814275	76.7102	64	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000833605.1	s__Anoxybacillus ayderensis	76.6823	61	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	97.55	97.17	0.91	0.88	8	-
GCF_018343625.1	s__FJAT-49711 sp018343625	76.6548	77	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829255.1	s__Metabacillus niabensis	76.6491	81	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_003315075.1	s__Rossellomorea aquimaris_C	76.6403	89	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355205.1	s__Lederbergia sp017355205	76.6336	61	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	95.07	95.07	0.86	0.86	2	-
GCF_003570725.1	s__Peribacillus asahii	76.5908	110	1072	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_001050115.1	s__Bacillus_O smithii	76.5865	82	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_O	95.0	98.56	97.85	0.91	0.87	4	-
GCF_018343715.1	s__FJAT-49711 sp018343715	76.4767	81	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380245.2	s__Bacillus_AD massiliogorillae	76.3971	82	1072	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_018343695.1	s__FJAT-49711 sp018343695	76.3486	86	1072	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:24,833] [INFO] GTDB search result was written to GCF_030813365.1_ASM3081336v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:24,834] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:24,839] [INFO] DFAST_QC result json was written to GCF_030813365.1_ASM3081336v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:24,839] [INFO] DFAST_QC completed!
[2024-01-25 19:57:24,839] [INFO] Total running time: 0h1m19s