[2024-01-24 11:35:34,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,568] [INFO] DQC Reference Directory: /var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference
[2024-01-24 11:35:35,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,764] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,764] [INFO] Running command: gunzip -c /var/lib/cwl/stga33221bd-76f6-4499-a8f3-4cd70084a9f2/GCF_018283675.1_ASM1828367v1_genomic.fna.gz | prodigal -d GCF_018283675.1_ASM1828367v1_genomic.fna/cds.fna -a GCF_018283675.1_ASM1828367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:45,320] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:45,320] [INFO] Task started: HMMsearch
[2024-01-24 11:35:45,321] [INFO] Running command: hmmsearch --tblout GCF_018283675.1_ASM1828367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference/reference_markers.hmm GCF_018283675.1_ASM1828367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:45,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:45,601] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga33221bd-76f6-4499-a8f3-4cd70084a9f2/GCF_018283675.1_ASM1828367v1_genomic.fna.gz]
[2024-01-24 11:35:45,639] [INFO] Query marker FASTA was written to GCF_018283675.1_ASM1828367v1_genomic.fna/markers.fasta
[2024-01-24 11:35:45,639] [INFO] Task started: Blastn
[2024-01-24 11:35:45,639] [INFO] Running command: blastn -query GCF_018283675.1_ASM1828367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference/reference_markers.fasta -out GCF_018283675.1_ASM1828367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:46,257] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:46,261] [INFO] Selected 19 target genomes.
[2024-01-24 11:35:46,262] [INFO] Target genome list was writen to GCF_018283675.1_ASM1828367v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:46,305] [INFO] Task started: fastANI
[2024-01-24 11:35:46,306] [INFO] Running command: fastANI --query /var/lib/cwl/stga33221bd-76f6-4499-a8f3-4cd70084a9f2/GCF_018283675.1_ASM1828367v1_genomic.fna.gz --refList GCF_018283675.1_ASM1828367v1_genomic.fna/target_genomes.txt --output GCF_018283675.1_ASM1828367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:59,316] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:59,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:59,332] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:59,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:59,332] [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
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	100.0	1342	1343	95	conclusive
Metabacillus mangrovi	strain=KCTC 33872	GCA_009711125.1	1491830	1491830	type	True	79.3181	520	1343	95	below_threshold
Bacillus mojavensis	strain=RO-H-1	GCA_000245335.1	72360	72360	type	True	78.8509	88	1343	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	78.2265	160	1343	95	below_threshold
Priestia abyssalis	strain=DSM 25875	GCA_002019595.1	1221450	1221450	type	True	78.0982	98	1343	95	below_threshold
Bacillus mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	77.5244	83	1343	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	77.4764	131	1343	95	below_threshold
Bacillus mojavensis	strain=RO-H-1	GCA_014499005.1	72360	72360	type	True	77.4574	83	1343	95	below_threshold
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	77.3342	116	1343	95	below_threshold
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	77.2981	148	1343	95	below_threshold
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	77.2087	147	1343	95	below_threshold
Bacillus velezensis	strain=KCTC 13012	GCA_001267695.1	492670	492670	type	True	77.1171	93	1343	95	below_threshold
Bacillus siamensis	strain=KCTC 13613	GCA_000262045.1	659243	659243	type	True	77.11	91	1343	95	below_threshold
Bacillus velezensis	strain=NRRL B-41580	GCA_001461825.1	492670	492670	type	True	77.1007	96	1343	95	below_threshold
Bacillus ectoiniformans	strain=DSM 28970	GCA_016908875.1	1494429	1494429	type	True	76.6195	63	1343	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	76.2932	81	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,334] [INFO] DFAST Taxonomy check result was written to GCF_018283675.1_ASM1828367v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:59,334] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:59,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:59,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference/checkm_data
[2024-01-24 11:35:59,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:59,373] [INFO] Task started: CheckM
[2024-01-24 11:35:59,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018283675.1_ASM1828367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018283675.1_ASM1828367v1_genomic.fna/checkm_input GCF_018283675.1_ASM1828367v1_genomic.fna/checkm_result
[2024-01-24 11:36:33,044] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:33,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:33,064] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:33,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:33,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018283675.1_ASM1828367v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:33,066] [INFO] Task started: Blastn
[2024-01-24 11:36:33,066] [INFO] Running command: blastn -query GCF_018283675.1_ASM1828367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35468731-10bb-445a-8ddf-2f3d8c10522d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018283675.1_ASM1828367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:33,908] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:33,912] [INFO] Selected 14 target genomes.
[2024-01-24 11:36:33,912] [INFO] Target genome list was writen to GCF_018283675.1_ASM1828367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:33,923] [INFO] Task started: fastANI
[2024-01-24 11:36:33,923] [INFO] Running command: fastANI --query /var/lib/cwl/stga33221bd-76f6-4499-a8f3-4cd70084a9f2/GCF_018283675.1_ASM1828367v1_genomic.fna.gz --refList GCF_018283675.1_ASM1828367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018283675.1_ASM1828367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:46,011] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:46,029] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:46,030] [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_018283675.1	s__Metabacillus_B sp018283675	100.0	1343	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000732485.2	s__Metabacillus_B sp000732485	90.7085	1177	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003816055.1	s__Metabacillus_B sp003816055	82.6917	918	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711125.1	s__Metabacillus_B mangrovi	79.2806	524	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518865.1	s__Metabacillus sp000518865	77.6715	87	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708755.2	s__Bacillus_P indicus	77.4764	131	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	-
GCF_001042475.2	s__Bacillus glycinifermentans	77.4397	72	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.06	95.94	0.90	0.86	8	-
GCF_003182355.1	s__Cytobacillus oceanisediminis_A	77.4173	84	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	77.3862	88	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674805.1	s__Metabacillus_C lacus	77.3337	116	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613235.1	s__Mesobacillus sp018613235	77.196	67	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674765.1	s__Bacillus_P idriensis	77.0891	144	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.40	95.01	0.92	0.87	5	-
GCF_001461825.1	s__Bacillus velezensis	77.0659	95	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
GCF_001591625.1	s__Metabacillus fastidiosus	76.3158	80	1343	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:46,031] [INFO] GTDB search result was written to GCF_018283675.1_ASM1828367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:46,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:46,039] [INFO] DFAST_QC result json was written to GCF_018283675.1_ASM1828367v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:46,039] [INFO] DFAST_QC completed!
[2024-01-24 11:36:46,039] [INFO] Total running time: 0h1m11s