[2024-01-25 19:55:20,734] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:20,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:20,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference
[2024-01-25 19:55:21,849] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:21,850] [INFO] Task started: Prodigal
[2024-01-25 19:55:21,850] [INFO] Running command: gunzip -c /var/lib/cwl/stgebab3c9d-9075-4502-a5ce-0e41460287f0/GCF_002019665.1_ASM201966v1_genomic.fna.gz | prodigal -d GCF_002019665.1_ASM201966v1_genomic.fna/cds.fna -a GCF_002019665.1_ASM201966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:30,280] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:30,281] [INFO] Task started: HMMsearch
[2024-01-25 19:55:30,281] [INFO] Running command: hmmsearch --tblout GCF_002019665.1_ASM201966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference/reference_markers.hmm GCF_002019665.1_ASM201966v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:30,570] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:30,571] [INFO] Found 6/6 markers.
[2024-01-25 19:55:30,609] [INFO] Query marker FASTA was written to GCF_002019665.1_ASM201966v1_genomic.fna/markers.fasta
[2024-01-25 19:55:30,610] [INFO] Task started: Blastn
[2024-01-25 19:55:30,610] [INFO] Running command: blastn -query GCF_002019665.1_ASM201966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference/reference_markers.fasta -out GCF_002019665.1_ASM201966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:31,179] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:31,181] [INFO] Selected 22 target genomes.
[2024-01-25 19:55:31,182] [INFO] Target genome list was writen to GCF_002019665.1_ASM201966v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:31,191] [INFO] Task started: fastANI
[2024-01-25 19:55:31,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgebab3c9d-9075-4502-a5ce-0e41460287f0/GCF_002019665.1_ASM201966v1_genomic.fna.gz --refList GCF_002019665.1_ASM201966v1_genomic.fna/target_genomes.txt --output GCF_002019665.1_ASM201966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:49,054] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:49,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:49,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:49,067] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:49,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:49,068] [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
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	100.0	1561	1566	95	conclusive
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	80.0875	427	1566	95	below_threshold
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	79.2574	57	1566	95	below_threshold
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	78.9522	54	1566	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	78.6969	252	1566	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	78.5662	257	1566	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.9687	112	1566	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	77.6916	237	1566	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.5024	100	1566	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	77.2866	115	1566	95	below_threshold
Rossellomorea arthrocnemi	strain=EAR8	GCA_904424705.1	2769542	2769542	type	True	77.1315	83	1566	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	77.062	88	1566	95	below_threshold
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	77.0198	93	1566	95	below_threshold
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	76.9257	92	1566	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.9167	112	1566	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.9045	109	1566	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	76.8998	60	1566	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.8955	109	1566	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	76.8049	56	1566	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.723	112	1566	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	76.5542	57	1566	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.5536	86	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:49,069] [INFO] DFAST Taxonomy check result was written to GCF_002019665.1_ASM201966v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:49,070] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:49,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:49,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference/checkm_data
[2024-01-25 19:55:49,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:49,117] [INFO] Task started: CheckM
[2024-01-25 19:55:49,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019665.1_ASM201966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019665.1_ASM201966v1_genomic.fna/checkm_input GCF_002019665.1_ASM201966v1_genomic.fna/checkm_result
[2024-01-25 19:56:17,777] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:17,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:17,795] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:17,796] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:17,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019665.1_ASM201966v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:17,796] [INFO] Task started: Blastn
[2024-01-25 19:56:17,796] [INFO] Running command: blastn -query GCF_002019665.1_ASM201966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbdca27-a085-4b79-9c5e-8a8b76cfe460/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019665.1_ASM201966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:18,534] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:18,537] [INFO] Selected 13 target genomes.
[2024-01-25 19:56:18,537] [INFO] Target genome list was writen to GCF_002019665.1_ASM201966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:18,543] [INFO] Task started: fastANI
[2024-01-25 19:56:18,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgebab3c9d-9075-4502-a5ce-0e41460287f0/GCF_002019665.1_ASM201966v1_genomic.fna.gz --refList GCF_002019665.1_ASM201966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019665.1_ASM201966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:31,337] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:31,345] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:31,346] [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_002019665.1	s__Sutcliffiella_A halmapala	100.0	1562	1566	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	conclusive
GCF_016908565.1	s__Sutcliffiella_A tianshenii	79.8829	510	1566	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	-
GCA_001636495.1	s__Sutcliffiella_A horikoshii_A	79.7369	415	1566	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_002157855.1	s__Sutcliffiella_A horikoshii_C	79.5261	435	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	96.53	95.82	0.92	0.90	4	-
GCF_008180725.1	s__Sutcliffiella_A horikoshii_B	79.4871	411	1566	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_001293645.1	s__Sutcliffiella_A sp001293645	79.4418	398	1566	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_012524115.1	s__Sutcliffiella_A sp012524115	79.3453	406	1566	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	-
GCA_001648575.1	s__Sutcliffiella_A horikoshii	79.3017	403	1566	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_012911845.1	s__Sutcliffiella_A sp012911845	79.268	408	1566	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_009363695.1	s__Sutcliffiella_A sp009363695	79.2421	352	1566	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_003667825.1	s__Metabacillus litoralis_B	78.8596	123	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002250055.1	s__Sutcliffiella cohnii	78.5662	257	1566	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_016908495.1	s__Bacillus_BW pakistanensis	76.7108	113	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BW	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:31,347] [INFO] GTDB search result was written to GCF_002019665.1_ASM201966v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:31,348] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:31,351] [INFO] DFAST_QC result json was written to GCF_002019665.1_ASM201966v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:31,351] [INFO] DFAST_QC completed!
[2024-01-25 19:56:31,351] [INFO] Total running time: 0h1m11s