[2024-01-24 12:23:34,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:34,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:34,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference
[2024-01-24 12:23:35,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:35,644] [INFO] Task started: Prodigal
[2024-01-24 12:23:35,645] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd7799d8-9031-41c5-ac3f-4c8337e8c753/GCF_002019595.1_ASM201959v1_genomic.fna.gz | prodigal -d GCF_002019595.1_ASM201959v1_genomic.fna/cds.fna -a GCF_002019595.1_ASM201959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:49,512] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:49,512] [INFO] Task started: HMMsearch
[2024-01-24 12:23:49,513] [INFO] Running command: hmmsearch --tblout GCF_002019595.1_ASM201959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference/reference_markers.hmm GCF_002019595.1_ASM201959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:49,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:49,805] [INFO] Found 6/6 markers.
[2024-01-24 12:23:49,848] [INFO] Query marker FASTA was written to GCF_002019595.1_ASM201959v1_genomic.fna/markers.fasta
[2024-01-24 12:23:49,848] [INFO] Task started: Blastn
[2024-01-24 12:23:49,849] [INFO] Running command: blastn -query GCF_002019595.1_ASM201959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference/reference_markers.fasta -out GCF_002019595.1_ASM201959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:50,434] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:50,438] [INFO] Selected 33 target genomes.
[2024-01-24 12:23:50,438] [INFO] Target genome list was writen to GCF_002019595.1_ASM201959v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:50,451] [INFO] Task started: fastANI
[2024-01-24 12:23:50,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd7799d8-9031-41c5-ac3f-4c8337e8c753/GCF_002019595.1_ASM201959v1_genomic.fna.gz --refList GCF_002019595.1_ASM201959v1_genomic.fna/target_genomes.txt --output GCF_002019595.1_ASM201959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:13,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:13,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:13,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:13,184] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:13,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:13,184] [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 abyssalis	strain=DSM 25875	GCA_002019595.1	1221450	1221450	type	True	100.0	1916	1922	95	conclusive
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.9319	112	1922	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.9188	108	1922	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	78.7848	106	1922	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	78.6604	109	1922	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	78.2827	86	1922	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	78.2476	81	1922	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	78.1434	88	1922	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	78.0891	229	1922	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	78.023	227	1922	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	77.6596	204	1922	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.6343	92	1922	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	77.6054	110	1922	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.4981	163	1922	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	77.4461	217	1922	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	77.3937	211	1922	95	below_threshold
Bacillus atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	77.3772	76	1922	95	below_threshold
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	77.3223	201	1922	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	77.2185	101	1922	95	below_threshold
Bacillus atrophaeus	strain=NBRC 15539	GCA_001591925.1	1452	1452	type	True	77.1345	79	1922	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	77.033	94	1922	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.0274	100	1922	95	below_threshold
Anoxybacillus karvacharensis	strain=K1	GCA_001996285.1	1919277	1919277	type	True	76.9512	95	1922	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.8145	84	1922	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.7344	73	1922	95	below_threshold
Anoxybacillus mongoliensis	strain=DSM 19169	GCA_014201515.1	452565	452565	type	True	76.7009	93	1922	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_001315165.1	308892	308892	type	True	76.6677	68	1922	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_000517385.1	308892	308892	type	True	76.6373	69	1922	95	below_threshold
Anoxybacillus tengchongensis	strain=DSM 23211	GCA_014201585.1	576944	576944	type	True	76.5632	98	1922	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	76.5372	95	1922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:13,186] [INFO] DFAST Taxonomy check result was written to GCF_002019595.1_ASM201959v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:13,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:13,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:13,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference/checkm_data
[2024-01-24 12:24:13,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:13,241] [INFO] Task started: CheckM
[2024-01-24 12:24:13,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019595.1_ASM201959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019595.1_ASM201959v1_genomic.fna/checkm_input GCF_002019595.1_ASM201959v1_genomic.fna/checkm_result
[2024-01-24 12:24:54,604] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:54,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:54,623] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:54,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:54,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019595.1_ASM201959v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:54,623] [INFO] Task started: Blastn
[2024-01-24 12:24:54,624] [INFO] Running command: blastn -query GCF_002019595.1_ASM201959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cad1a67-4ded-49f4-9ee3-66bf6985c232/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019595.1_ASM201959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:55,385] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:55,389] [INFO] Selected 27 target genomes.
[2024-01-24 12:24:55,389] [INFO] Target genome list was writen to GCF_002019595.1_ASM201959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:55,413] [INFO] Task started: fastANI
[2024-01-24 12:24:55,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd7799d8-9031-41c5-ac3f-4c8337e8c753/GCF_002019595.1_ASM201959v1_genomic.fna.gz --refList GCF_002019595.1_ASM201959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019595.1_ASM201959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:18,907] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:18,925] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:18,925] [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_002019595.1	s__Bacillus_BA abyssalis	100.0	1916	1922	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	conclusive
GCF_000504165.1	s__Bacillus_BA sp000504165	89.9009	1398	1922	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_001636315.1	s__Neobacillus mesonae	78.9132	110	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_002250055.1	s__Sutcliffiella cohnii	78.7926	111	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCF_001636425.1	s__Bacillus_AE acidicola	78.1986	104	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180335.1	s__Priestia megaterium_B	78.1663	215	1922	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_000832985.1	s__Priestia megaterium	77.9939	230	1922	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_003184905.1	s__Priestia sp003184905	77.8406	215	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	77.7467	140	1922	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_000299035.1	s__Bacillus_A bingmayongensis	77.6765	131	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	-
GCF_002835735.1	s__Cytobacillus horneckiae	77.6703	91	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_016909075.1	s__Priestia iocasae	77.6532	203	1922	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_902829255.1	s__Metabacillus niabensis	77.5534	115	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_004358205.1	s__Neobacillus salipaludis	77.5135	162	1922	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_018343715.1	s__FJAT-49711 sp018343715	77.4652	69	1922	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_900112415.1	s__Bacillus_A sp900112415	77.4453	137	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.00	99.00	0.93	0.93	2	-
GCF_001584335.1	s__Bacillus atrophaeus	77.3772	76	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.59	97.38	0.93	0.89	38	-
GCF_001274935.1	s__Bacillus_AG koreensis	77.3674	171	1922	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_000956595.1	s__Priestia aryabhattai	77.31	202	1922	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_003259935.1	s__Anoxybacillus_B vitaminiphilus	77.0041	140	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439915.1	s__Fredinandcohnia humi	76.9292	102	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668575.1	s__Falsibacillus albus	76.7344	73	1922	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_014201515.1	s__Anoxybacillus mongoliensis	76.7333	92	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201585.1	s__Anoxybacillus tengchongensis	76.5414	99	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:18,927] [INFO] GTDB search result was written to GCF_002019595.1_ASM201959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:18,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:18,933] [INFO] DFAST_QC result json was written to GCF_002019595.1_ASM201959v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:18,933] [INFO] DFAST_QC completed!
[2024-01-24 12:25:18,933] [INFO] Total running time: 0h1m45s