[2024-01-24 11:50:49,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference
[2024-01-24 11:50:50,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,532] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg00acd4be-ece1-4499-a74e-40257c97f830/GCF_000712595.1_ASM71259v1_genomic.fna.gz | prodigal -d GCF_000712595.1_ASM71259v1_genomic.fna/cds.fna -a GCF_000712595.1_ASM71259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:50:59,766] [INFO] Task succeeded: Prodigal
[2024-01-24 11:50:59,767] [INFO] Task started: HMMsearch
[2024-01-24 11:50:59,767] [INFO] Running command: hmmsearch --tblout GCF_000712595.1_ASM71259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference/reference_markers.hmm GCF_000712595.1_ASM71259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:00,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:00,054] [INFO] Found 6/6 markers.
[2024-01-24 11:51:00,101] [INFO] Query marker FASTA was written to GCF_000712595.1_ASM71259v1_genomic.fna/markers.fasta
[2024-01-24 11:51:00,102] [INFO] Task started: Blastn
[2024-01-24 11:51:00,102] [INFO] Running command: blastn -query GCF_000712595.1_ASM71259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference/reference_markers.fasta -out GCF_000712595.1_ASM71259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:00,732] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:00,736] [INFO] Selected 21 target genomes.
[2024-01-24 11:51:00,736] [INFO] Target genome list was writen to GCF_000712595.1_ASM71259v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:01,418] [INFO] Task started: fastANI
[2024-01-24 11:51:01,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg00acd4be-ece1-4499-a74e-40257c97f830/GCF_000712595.1_ASM71259v1_genomic.fna.gz --refList GCF_000712595.1_ASM71259v1_genomic.fna/target_genomes.txt --output GCF_000712595.1_ASM71259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:18,806] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:18,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:18,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:18,825] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:18,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:18,825] [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=KCTC 13318	GCA_001590835.1	574375	574375	type	True	80.6134	660	1503	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	80.5779	659	1503	95	below_threshold
Bacillus toyonensis	strain=BCT-7112	GCA_000496285.1	155322	155322	type	True	80.5019	622	1503	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	80.4796	672	1503	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	80.4643	642	1503	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	80.452	641	1503	95	below_threshold
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	80.437	637	1503	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	80.4201	679	1503	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	80.3832	643	1503	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	80.3828	635	1503	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	80.348	608	1503	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	80.2979	640	1503	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	80.2923	662	1503	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	80.2743	647	1503	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	80.2082	678	1503	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	80.017	572	1503	95	below_threshold
Ectobacillus antri	strain=SYSU K30001	GCA_003852715.1	2486280	2486280	type	True	77.8047	184	1503	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	77.3192	144	1503	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.8406	102	1503	95	below_threshold
Bacillus oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	76.715	52	1503	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	76.3399	71	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:18,827] [INFO] DFAST Taxonomy check result was written to GCF_000712595.1_ASM71259v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:18,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:18,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:18,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference/checkm_data
[2024-01-24 11:51:18,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:18,874] [INFO] Task started: CheckM
[2024-01-24 11:51:18,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000712595.1_ASM71259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000712595.1_ASM71259v1_genomic.fna/checkm_input GCF_000712595.1_ASM71259v1_genomic.fna/checkm_result
[2024-01-24 11:51:51,507] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:51,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:51,530] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:51,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:51,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000712595.1_ASM71259v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:51,532] [INFO] Task started: Blastn
[2024-01-24 11:51:51,532] [INFO] Running command: blastn -query GCF_000712595.1_ASM71259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg782e3ae7-d19f-4b55-9998-bba9379db096/dqc_reference/reference_markers_gtdb.fasta -out GCF_000712595.1_ASM71259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:52,319] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:52,324] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:52,324] [INFO] Target genome list was writen to GCF_000712595.1_ASM71259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:52,334] [INFO] Task started: fastANI
[2024-01-24 11:51:52,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg00acd4be-ece1-4499-a74e-40257c97f830/GCF_000712595.1_ASM71259v1_genomic.fna.gz --refList GCF_000712595.1_ASM71259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000712595.1_ASM71259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:07,600] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:07,617] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:07,618] [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_000712595.1	s__Bacillus_A manliponensis	100.0	1499	1503	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	conclusive
GCF_002560985.1	s__Bacillus_A sp002560985	81.0025	675	1503	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_002551005.1	s__Bacillus_A pseudomycoides_C	80.897	637	1503	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_000383235.1	s__Bacillus_A sp000383235	80.8436	602	1503	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_900116295.1	s__Bacillus_A sp900116295	80.7945	680	1503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	80.7826	696	1503	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_900112415.1	s__Bacillus_A sp900112415	80.7733	635	1503	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_013314535.1	s__Bacillus_A sp013314535	80.6992	721	1503	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_000299035.1	s__Bacillus_A bingmayongensis	80.6825	696	1503	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_002584535.1	s__Bacillus_A cereus_AW	80.6664	667	1503	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	-
GCF_002559665.1	s__Bacillus_A cereus_AV	80.6519	671	1503	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_002551815.1	s__Bacillus_A sp002551815	80.6225	642	1503	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	80.6076	660	1503	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_000161455.1	s__Bacillus_A pseudomycoides	80.5403	691	1503	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_000746925.1	s__Bacillus_A clarus	80.4287	678	1503	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:07,619] [INFO] GTDB search result was written to GCF_000712595.1_ASM71259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:07,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:07,626] [INFO] DFAST_QC result json was written to GCF_000712595.1_ASM71259v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:07,627] [INFO] DFAST_QC completed!
[2024-01-24 11:52:07,627] [INFO] Total running time: 0h1m18s