[2024-01-24 12:42:09,849] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,851] [INFO] DQC Reference Directory: /var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference
[2024-01-24 12:42:11,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:11,112] [INFO] Task started: Prodigal
[2024-01-24 12:42:11,112] [INFO] Running command: gunzip -c /var/lib/cwl/stg83eef61c-daa3-42ec-8256-7c9b205f50e3/GCF_028610705.1_ASM2861070v1_genomic.fna.gz | prodigal -d GCF_028610705.1_ASM2861070v1_genomic.fna/cds.fna -a GCF_028610705.1_ASM2861070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:21,342] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:21,342] [INFO] Task started: HMMsearch
[2024-01-24 12:42:21,342] [INFO] Running command: hmmsearch --tblout GCF_028610705.1_ASM2861070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference/reference_markers.hmm GCF_028610705.1_ASM2861070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:21,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:21,666] [INFO] Found 6/6 markers.
[2024-01-24 12:42:21,716] [INFO] Query marker FASTA was written to GCF_028610705.1_ASM2861070v1_genomic.fna/markers.fasta
[2024-01-24 12:42:21,716] [INFO] Task started: Blastn
[2024-01-24 12:42:21,717] [INFO] Running command: blastn -query GCF_028610705.1_ASM2861070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference/reference_markers.fasta -out GCF_028610705.1_ASM2861070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:22,316] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:22,323] [INFO] Selected 20 target genomes.
[2024-01-24 12:42:22,324] [INFO] Target genome list was writen to GCF_028610705.1_ASM2861070v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:22,332] [INFO] Task started: fastANI
[2024-01-24 12:42:22,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg83eef61c-daa3-42ec-8256-7c9b205f50e3/GCF_028610705.1_ASM2861070v1_genomic.fna.gz --refList GCF_028610705.1_ASM2861070v1_genomic.fna/target_genomes.txt --output GCF_028610705.1_ASM2861070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:35,033] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:35,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:35,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:35,055] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:42:35,055] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:42:35,055] [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
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	79.8269	564	1699	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	79.8214	565	1699	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	79.572	530	1699	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	79.4465	530	1699	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	78.9749	389	1699	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	78.9595	390	1699	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	78.9525	474	1699	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.4347	288	1699	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	78.0908	253	1699	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.0506	157	1699	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	76.9595	130	1699	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.4193	50	1699	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	76.2001	74	1699	95	below_threshold
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	76.1621	72	1699	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	76.1316	73	1699	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	76.1051	72	1699	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	75.9109	50	1699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:35,058] [INFO] DFAST Taxonomy check result was written to GCF_028610705.1_ASM2861070v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:35,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:35,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:35,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference/checkm_data
[2024-01-24 12:42:35,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:35,118] [INFO] Task started: CheckM
[2024-01-24 12:42:35,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028610705.1_ASM2861070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028610705.1_ASM2861070v1_genomic.fna/checkm_input GCF_028610705.1_ASM2861070v1_genomic.fna/checkm_result
[2024-01-24 12:43:10,639] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:10,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:10,663] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:10,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:10,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028610705.1_ASM2861070v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:10,664] [INFO] Task started: Blastn
[2024-01-24 12:43:10,664] [INFO] Running command: blastn -query GCF_028610705.1_ASM2861070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec871aba-dd2e-4f05-96c0-7c2f455cdd6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_028610705.1_ASM2861070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:11,424] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:11,428] [INFO] Selected 16 target genomes.
[2024-01-24 12:43:11,429] [INFO] Target genome list was writen to GCF_028610705.1_ASM2861070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:11,441] [INFO] Task started: fastANI
[2024-01-24 12:43:11,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg83eef61c-daa3-42ec-8256-7c9b205f50e3/GCF_028610705.1_ASM2861070v1_genomic.fna.gz --refList GCF_028610705.1_ASM2861070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028610705.1_ASM2861070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:23,319] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:23,332] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:43:23,332] [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_000513135.1	s__Bacillus_L akibai	79.8023	567	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002109385.1	s__Bacillus_L krulwichiae	79.5826	526	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000513095.1	s__Bacillus_L wakoensis	78.9886	386	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000787375.1	s__Bacillus_L okhensis	78.944	472	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.4462	287	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	78.0957	252	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000334155.1	s__Bacillus_AN ligniniphilus	77.5567	128	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.0489	156	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	76.9702	130	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	76.9405	148	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383235.1	s__Bacillus_A sp000383235	76.6898	69	1699	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_002574955.1	s__Bacillus_A cereus_AT	76.2843	73	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.1182	99.26	96.80	0.94	0.81	6	-
GCF_001708185.1	s__Lysinibacillus xylanilyticus_A	76.2224	55	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001308875.1	s__Lysinibacillus sp001308875	76.2005	59	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002567495.1	s__Bacillus_A cereus_AQ	76.0959	73	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.10	96.80	0.92	0.88	3	-
GCF_009724685.1	s__Lysinibacillus sp009724685	75.9109	50	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:23,334] [INFO] GTDB search result was written to GCF_028610705.1_ASM2861070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:23,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:23,340] [INFO] DFAST_QC result json was written to GCF_028610705.1_ASM2861070v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:23,340] [INFO] DFAST_QC completed!
[2024-01-24 12:43:23,340] [INFO] Total running time: 0h1m13s