[2024-01-24 14:07:14,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference
[2024-01-24 14:07:15,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:15,821] [INFO] Task started: Prodigal
[2024-01-24 14:07:15,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg05330c09-bca6-402e-a247-4bb52ec2fa5d/GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna.gz | prodigal -d GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/cds.fna -a GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:27,432] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:27,432] [INFO] Task started: HMMsearch
[2024-01-24 14:07:27,432] [INFO] Running command: hmmsearch --tblout GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference/reference_markers.hmm GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:27,750] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:27,752] [INFO] Found 6/6 markers.
[2024-01-24 14:07:27,797] [INFO] Query marker FASTA was written to GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/markers.fasta
[2024-01-24 14:07:27,797] [INFO] Task started: Blastn
[2024-01-24 14:07:27,797] [INFO] Running command: blastn -query GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/markers.fasta -db /var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference/reference_markers.fasta -out GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:28,417] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:28,421] [INFO] Selected 21 target genomes.
[2024-01-24 14:07:28,422] [INFO] Target genome list was writen to GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/target_genomes.txt
[2024-01-24 14:07:28,430] [INFO] Task started: fastANI
[2024-01-24 14:07:28,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg05330c09-bca6-402e-a247-4bb52ec2fa5d/GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna.gz --refList GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/target_genomes.txt --output GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:43,957] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:43,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:43,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:43,977] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:43,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:43,977] [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
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	81.8982	829	1615	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.2761	291	1615	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.2336	381	1615	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.2236	403	1615	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.0059	328	1615	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.9464	333	1615	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.8727	274	1615	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.8585	309	1615	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	77.8554	326	1615	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.7292	248	1615	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.7165	322	1615	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.4985	313	1615	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	77.4493	261	1615	95	below_threshold
Bacillus siamensis	strain=KCTC 13613	GCA_000262045.1	659243	659243	type	True	77.1978	53	1615	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.0708	56	1615	95	below_threshold
Neobacillus piezotolerans	strain=YLB-04	GCA_003362805.1	2259171	2259171	type	True	77.0269	97	1615	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.6418	131	1615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:43,979] [INFO] DFAST Taxonomy check result was written to GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/tc_result.tsv
[2024-01-24 14:07:43,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:43,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:43,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference/checkm_data
[2024-01-24 14:07:43,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:44,030] [INFO] Task started: CheckM
[2024-01-24 14:07:44,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/checkm_input GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/checkm_result
[2024-01-24 14:08:22,275] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:22,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:22,294] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:22,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:22,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/markers.fasta)
[2024-01-24 14:08:22,295] [INFO] Task started: Blastn
[2024-01-24 14:08:22,295] [INFO] Running command: blastn -query GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/markers.fasta -db /var/lib/cwl/stg42910fbb-3b29-4519-95de-632654abdc97/dqc_reference/reference_markers_gtdb.fasta -out GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:23,114] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:23,117] [INFO] Selected 20 target genomes.
[2024-01-24 14:08:23,118] [INFO] Target genome list was writen to GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:23,151] [INFO] Task started: fastANI
[2024-01-24 14:08:23,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg05330c09-bca6-402e-a247-4bb52ec2fa5d/GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna.gz --refList GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/target_genomes_gtdb.txt --output GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:43,754] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:43,770] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:08:43,770] [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_000612665.1	s__Neobacillus dielmonensis	81.898	829	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908975.1	s__Neobacillus cucumis	78.2761	291	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613415.1	s__Neobacillus sp018613415	78.2262	334	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343535.1	s__Neobacillus sp018343535	78.225	404	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_001510715.1	s__Neobacillus sp001510715	78.2222	367	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765675.1	s__Neobacillus sp016765675	78.1381	286	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005154805.1	s__Neobacillus sp005154805	78.0775	348	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001026695.1	s__Neobacillus vireti	77.9975	327	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001636315.1	s__Neobacillus mesonae	77.9766	334	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_018613065.1	s__Neobacillus sp018613065	77.9353	313	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_016464375.1	s__Neobacillus renqingensis	77.8808	294	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048695.1	s__Neobacillus massiliamazoniensis	77.8768	273	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482325.1	s__Neobacillus sp000482325	77.8255	281	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975035.1	s__Neobacillus thermocopriae	77.7423	247	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_016107705.1	s__Neobacillus cucumis_B	77.6922	289	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591665.1	s__Neobacillus soli	77.5222	311	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001509555.1	s__Cytobacillus sp001509555	77.1224	125	1615	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_000169195.2	s__Weizmannia coagulans_A	76.4614	53	1615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	98.29	97.76	0.92	0.89	29	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:43,772] [INFO] GTDB search result was written to GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:43,772] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:43,776] [INFO] DFAST_QC result json was written to GCF_943193175.1_Neobacillus_sp_nov_DSM110989_genomic.fna/dqc_result.json
[2024-01-24 14:08:43,777] [INFO] DFAST_QC completed!
[2024-01-24 14:08:43,777] [INFO] Total running time: 0h1m29s