[2024-01-24 11:12:25,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:25,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:25,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference
[2024-01-24 11:12:27,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,114] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf967648-e23d-4dd9-881d-36a0e9bf37ea/GCF_018343545.2_ASM1834354v2_genomic.fna.gz | prodigal -d GCF_018343545.2_ASM1834354v2_genomic.fna/cds.fna -a GCF_018343545.2_ASM1834354v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:40,256] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:40,256] [INFO] Task started: HMMsearch
[2024-01-24 11:12:40,257] [INFO] Running command: hmmsearch --tblout GCF_018343545.2_ASM1834354v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference/reference_markers.hmm GCF_018343545.2_ASM1834354v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:40,638] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:40,639] [INFO] Found 6/6 markers.
[2024-01-24 11:12:40,697] [INFO] Query marker FASTA was written to GCF_018343545.2_ASM1834354v2_genomic.fna/markers.fasta
[2024-01-24 11:12:40,698] [INFO] Task started: Blastn
[2024-01-24 11:12:40,698] [INFO] Running command: blastn -query GCF_018343545.2_ASM1834354v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference/reference_markers.fasta -out GCF_018343545.2_ASM1834354v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:41,369] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:41,373] [INFO] Selected 21 target genomes.
[2024-01-24 11:12:41,373] [INFO] Target genome list was writen to GCF_018343545.2_ASM1834354v2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:41,386] [INFO] Task started: fastANI
[2024-01-24 11:12:41,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf967648-e23d-4dd9-881d-36a0e9bf37ea/GCF_018343545.2_ASM1834354v2_genomic.fna.gz --refList GCF_018343545.2_ASM1834354v2_genomic.fna/target_genomes.txt --output GCF_018343545.2_ASM1834354v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:02,115] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:02,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:02,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:02,131] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:02,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:02,132] [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 citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	100.0	1925	1939	95	conclusive
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	93.4396	1573	1939	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.9237	515	1939	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	78.5493	435	1939	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.5083	458	1939	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	78.4543	342	1939	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	78.4526	480	1939	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.3836	517	1939	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	78.3313	380	1939	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.2771	403	1939	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	78.2679	409	1939	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	78.2002	334	1939	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	78.1885	344	1939	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	78.0995	371	1939	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.5569	274	1939	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	77.3195	133	1939	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.1634	166	1939	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1176	111	1939	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.8564	105	1939	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	76.3706	59	1939	95	below_threshold
Domibacillus robiginosus	strain=WS 4628	GCA_000966195.1	1071054	1071054	type	True	76.2254	67	1939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:02,133] [INFO] DFAST Taxonomy check result was written to GCF_018343545.2_ASM1834354v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:02,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:02,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:02,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference/checkm_data
[2024-01-24 11:13:02,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:02,198] [INFO] Task started: CheckM
[2024-01-24 11:13:02,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018343545.2_ASM1834354v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018343545.2_ASM1834354v2_genomic.fna/checkm_input GCF_018343545.2_ASM1834354v2_genomic.fna/checkm_result
[2024-01-24 11:13:44,975] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:44,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:45,003] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:45,004] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:45,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018343545.2_ASM1834354v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:45,005] [INFO] Task started: Blastn
[2024-01-24 11:13:45,005] [INFO] Running command: blastn -query GCF_018343545.2_ASM1834354v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a1afd96-b7d3-4fb1-9970-ac7a57f8eecd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018343545.2_ASM1834354v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:45,810] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:45,814] [INFO] Selected 27 target genomes.
[2024-01-24 11:13:45,814] [INFO] Target genome list was writen to GCF_018343545.2_ASM1834354v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:45,844] [INFO] Task started: fastANI
[2024-01-24 11:13:45,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf967648-e23d-4dd9-881d-36a0e9bf37ea/GCF_018343545.2_ASM1834354v2_genomic.fna.gz --refList GCF_018343545.2_ASM1834354v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018343545.2_ASM1834354v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:20,189] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:20,220] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:20,221] [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_018343535.1	s__Neobacillus sp018343535	93.4271	1575	1939	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	79.5406	616	1939	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_001636315.1	s__Neobacillus mesonae	78.8766	520	1939	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_005154805.1	s__Neobacillus sp005154805	78.8572	481	1939	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_016107705.1	s__Neobacillus cucumis_B	78.6895	423	1939	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_004358205.1	s__Neobacillus salipaludis	78.644	410	1939	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_002860255.1	s__Neobacillus cucumis_A	78.633	426	1939	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_001866655.1	s__Neobacillus sp001866655	78.5622	416	1939	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	78.5267	385	1939	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_001591805.1	s__Neobacillus novalis	78.5246	436	1939	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_000612665.1	s__Neobacillus dielmonensis	78.5181	336	1939	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	78.4582	425	1939	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_000307875.1	s__Neobacillus bataviensis	78.4546	478	1939	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_002585305.1	s__Neobacillus sp002585305	78.4167	437	1939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_014656545.1	s__Neobacillus sp014656545	78.3866	516	1939	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	-
GCA_019219025.1	s__Neobacillus sp019219025	78.3226	444	1939	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_018613065.1	s__Neobacillus sp018613065	78.3157	451	1939	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_016908975.1	s__Neobacillus cucumis	78.3124	400	1939	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_000759675.1	s__Neobacillus niacini_A	78.2521	366	1939	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_000612625.1	s__Neobacillus jeddahensis	78.2128	352	1939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_010975035.1	s__Neobacillus thermocopriae	78.1988	342	1939	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_900177675.1	s__Neobacillus sp900177675	78.1343	484	1939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_013248975.1	s__Neobacillus endophyticus	78.1181	368	1939	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	77.887	330	1939	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_016464375.1	s__Neobacillus renqingensis	77.8088	354	1939	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_001591485.1	s__Neobacillus fumarioli	77.5462	275	1939	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_001509555.1	s__Cytobacillus sp001509555	77.276	169	1939	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:20,222] [INFO] GTDB search result was written to GCF_018343545.2_ASM1834354v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:20,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:20,228] [INFO] DFAST_QC result json was written to GCF_018343545.2_ASM1834354v2_genomic.fna/dqc_result.json
[2024-01-24 11:14:20,228] [INFO] DFAST_QC completed!
[2024-01-24 11:14:20,229] [INFO] Total running time: 0h1m54s