[2024-01-24 14:22:01,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference
[2024-01-24 14:22:02,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,871] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg823151ed-d7cf-4e11-8356-d4aefb8a461d/GCF_017498775.1_ASM1749877v1_genomic.fna.gz | prodigal -d GCF_017498775.1_ASM1749877v1_genomic.fna/cds.fna -a GCF_017498775.1_ASM1749877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:12,769] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:12,769] [INFO] Task started: HMMsearch
[2024-01-24 14:22:12,770] [INFO] Running command: hmmsearch --tblout GCF_017498775.1_ASM1749877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference/reference_markers.hmm GCF_017498775.1_ASM1749877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:13,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:13,098] [INFO] Found 6/6 markers.
[2024-01-24 14:22:13,139] [INFO] Query marker FASTA was written to GCF_017498775.1_ASM1749877v1_genomic.fna/markers.fasta
[2024-01-24 14:22:13,139] [INFO] Task started: Blastn
[2024-01-24 14:22:13,139] [INFO] Running command: blastn -query GCF_017498775.1_ASM1749877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference/reference_markers.fasta -out GCF_017498775.1_ASM1749877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:13,813] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:13,817] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:13,817] [INFO] Target genome list was writen to GCF_017498775.1_ASM1749877v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:13,828] [INFO] Task started: fastANI
[2024-01-24 14:22:13,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg823151ed-d7cf-4e11-8356-d4aefb8a461d/GCF_017498775.1_ASM1749877v1_genomic.fna.gz --refList GCF_017498775.1_ASM1749877v1_genomic.fna/target_genomes.txt --output GCF_017498775.1_ASM1749877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:34,939] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:34,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:34,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:34,955] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:34,955] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:34,955] [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
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	86.2652	1210	1677	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	86.2515	1221	1677	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	84.5581	1147	1677	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	84.5373	1160	1677	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	83.4367	1097	1677	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	83.4285	991	1677	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	83.4224	1103	1677	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	83.4077	1096	1677	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	83.3367	997	1677	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	83.2816	1013	1677	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	83.2344	999	1677	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	83.2231	1000	1677	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	83.2045	991	1677	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	83.1962	915	1677	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	83.1723	890	1677	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	83.1565	995	1677	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	77.6404	52	1677	95	below_threshold
Mangrovibacillus cuniculi	strain=R1DC41	GCA_015482585.1	2593652	2593652	type	True	76.9303	76	1677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:34,957] [INFO] DFAST Taxonomy check result was written to GCF_017498775.1_ASM1749877v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:34,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:34,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:34,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference/checkm_data
[2024-01-24 14:22:34,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:35,014] [INFO] Task started: CheckM
[2024-01-24 14:22:35,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017498775.1_ASM1749877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017498775.1_ASM1749877v1_genomic.fna/checkm_input GCF_017498775.1_ASM1749877v1_genomic.fna/checkm_result
[2024-01-24 14:23:09,709] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:09,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:09,730] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:09,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:09,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017498775.1_ASM1749877v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:09,731] [INFO] Task started: Blastn
[2024-01-24 14:23:09,731] [INFO] Running command: blastn -query GCF_017498775.1_ASM1749877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f3c998-489b-4c00-b223-ae2d1ba712f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017498775.1_ASM1749877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:10,601] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:10,604] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:10,604] [INFO] Target genome list was writen to GCF_017498775.1_ASM1749877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:10,615] [INFO] Task started: fastANI
[2024-01-24 14:23:10,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg823151ed-d7cf-4e11-8356-d4aefb8a461d/GCF_017498775.1_ASM1749877v1_genomic.fna.gz --refList GCF_017498775.1_ASM1749877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017498775.1_ASM1749877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:27,016] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:27,027] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:27,027] [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_002584535.1	s__Bacillus_A cereus_AW	98.2428	1490	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	conclusive
GCF_002559665.1	s__Bacillus_A cereus_AV	90.4918	1372	1677	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_000161455.1	s__Bacillus_A pseudomycoides	90.1109	1387	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.62	95.81	0.91	0.85	116	-
GCF_000299035.1	s__Bacillus_A bingmayongensis	89.5698	1292	1677	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_013314535.1	s__Bacillus_A sp013314535	89.203	1294	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
GCF_002561295.1	s__Bacillus_A cereus_S	88.5149	1253	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.16	96.34	0.94	0.87	9	-
GCF_002551815.1	s__Bacillus_A sp002551815	86.6668	1125	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
GCF_001590835.1	s__Bacillus_A gaemokensis	86.2399	1222	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000746925.1	s__Bacillus_A clarus	84.5265	1160	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001757995.1	s__Bacillus_A mycoides_B	83.8298	1122	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.94	99.86	0.98	0.98	4	-
GCF_007673305.1	s__Bacillus_A mycoides_C	83.5526	1016	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.83	95.78	0.82	0.81	3	-
GCF_002584985.1	s__Bacillus_A sp002584985	83.4757	1023	1677	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.52	99.41	0.96	0.94	8	-
GCF_002571225.1	s__Bacillus_A sp002571225	83.173	1022	1677	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:27,036] [INFO] GTDB search result was written to GCF_017498775.1_ASM1749877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:27,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:27,041] [INFO] DFAST_QC result json was written to GCF_017498775.1_ASM1749877v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:27,041] [INFO] DFAST_QC completed!
[2024-01-24 14:23:27,041] [INFO] Total running time: 0h1m25s