[2024-01-24 13:22:31,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference
[2024-01-24 13:22:33,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:33,080] [INFO] Task started: Prodigal
[2024-01-24 13:22:33,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgd68ab45c-84e5-4a33-8505-85bfa1e6dc32/GCF_013343715.1_ASM1334371v1_genomic.fna.gz | prodigal -d GCF_013343715.1_ASM1334371v1_genomic.fna/cds.fna -a GCF_013343715.1_ASM1334371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:42,747] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:42,748] [INFO] Task started: HMMsearch
[2024-01-24 13:22:42,748] [INFO] Running command: hmmsearch --tblout GCF_013343715.1_ASM1334371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference/reference_markers.hmm GCF_013343715.1_ASM1334371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:43,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:43,055] [INFO] Found 6/6 markers.
[2024-01-24 13:22:43,100] [INFO] Query marker FASTA was written to GCF_013343715.1_ASM1334371v1_genomic.fna/markers.fasta
[2024-01-24 13:22:43,101] [INFO] Task started: Blastn
[2024-01-24 13:22:43,101] [INFO] Running command: blastn -query GCF_013343715.1_ASM1334371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference/reference_markers.fasta -out GCF_013343715.1_ASM1334371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:43,682] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:43,685] [INFO] Selected 25 target genomes.
[2024-01-24 13:22:43,685] [INFO] Target genome list was writen to GCF_013343715.1_ASM1334371v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:45,149] [INFO] Task started: fastANI
[2024-01-24 13:22:45,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgd68ab45c-84e5-4a33-8505-85bfa1e6dc32/GCF_013343715.1_ASM1334371v1_genomic.fna.gz --refList GCF_013343715.1_ASM1334371v1_genomic.fna/target_genomes.txt --output GCF_013343715.1_ASM1334371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:03,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:03,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:03,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:03,278] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:03,278] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:03,278] [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
Mesobacillus harenae	strain=Y40	GCA_013343715.1	2213203	2213203	type	True	100.0	1529	1533	95	conclusive
Mesobacillus zeae	strain=JJ-247	GCA_013618945.1	1917180	1917180	type	True	78.0124	140	1533	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	77.7308	141	1533	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.6985	147	1533	95	below_threshold
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	77.5508	172	1533	95	below_threshold
Mesobacillus jeotgali	strain=DSM 18226	GCA_002874535.1	129985	129985	type	True	77.5168	173	1533	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	77.5122	83	1533	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.4764	117	1533	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	77.4534	91	1533	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.3631	138	1533	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	77.2942	166	1533	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	77.2896	84	1533	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	77.1968	102	1533	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.1863	147	1533	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.1573	110	1533	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	77.0537	143	1533	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.0113	133	1533	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	76.8654	124	1533	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.7855	88	1533	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.7432	128	1533	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	76.0855	51	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:03,280] [INFO] DFAST Taxonomy check result was written to GCF_013343715.1_ASM1334371v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:03,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:03,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:03,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference/checkm_data
[2024-01-24 13:23:03,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:03,327] [INFO] Task started: CheckM
[2024-01-24 13:23:03,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013343715.1_ASM1334371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013343715.1_ASM1334371v1_genomic.fna/checkm_input GCF_013343715.1_ASM1334371v1_genomic.fna/checkm_result
[2024-01-24 13:23:36,954] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:36,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,974] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:36,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:36,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013343715.1_ASM1334371v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:36,976] [INFO] Task started: Blastn
[2024-01-24 13:23:36,976] [INFO] Running command: blastn -query GCF_013343715.1_ASM1334371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6502dfaf-97f2-4363-ae56-18b6d67cb7ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_013343715.1_ASM1334371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:37,773] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:37,777] [INFO] Selected 28 target genomes.
[2024-01-24 13:23:37,777] [INFO] Target genome list was writen to GCF_013343715.1_ASM1334371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:38,459] [INFO] Task started: fastANI
[2024-01-24 13:23:38,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgd68ab45c-84e5-4a33-8505-85bfa1e6dc32/GCF_013343715.1_ASM1334371v1_genomic.fna.gz --refList GCF_013343715.1_ASM1334371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013343715.1_ASM1334371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:00,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:01,013] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:01,014] [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_013343715.1	s__Mesobacillus_A harenae	100.0	1529	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104575.1	s__Bacillus_BD tuaregi	77.8616	102	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003570705.1	s__Bacillus_AZ zeae	77.752	140	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	100.00	100.00	1.00	1.00	3	-
GCF_007678455.1	s__Mesobacillus oceanisediminis_A	77.6394	161	1533	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_018613155.1	s__Mesobacillus sp018613155	77.5875	164	1533	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_002860205.1	s__T33-2 sp002860205	77.5248	178	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__T33-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002874535.1	s__Mesobacillus jeotgali	77.5153	173	1533	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_018613315.1	s__Mesobacillus sp018613315	77.4528	171	1533	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_002860165.1	s__Bacillus_BJ sp002860165	77.4084	121	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613235.1	s__Mesobacillus sp018613235	77.408	170	1533	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_018613195.1	s__Mesobacillus sp018613195	77.3752	161	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	98.95	98.95	0.85	0.85	2	-
GCF_000986785.1	s__Bacillus_AZ campisalis	77.3502	165	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011393025.1	s__URHB0009 sp011393025	77.3162	134	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163115.1	s__Mesobacillus selenatarsenatis_A	77.3089	158	1533	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_001273925.1	s__Bacillus_AZ sp001273925	77.2962	156	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183415.1	s__Niallia sp009183415	77.2807	77	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917645.1	s__Robertmurraya sp009917645	77.2683	138	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909175.1	s__Bacillus_AI deserti	77.2408	102	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	77.1954	149	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000262755.1	s__Bacillus_Z methanolicus	77.0527	143	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358205.1	s__Neobacillus salipaludis	77.0113	130	1533	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	76.9584	135	1533	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_000686805.1	s__Neobacillus sp000686805	76.9548	121	1533	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_000518885.1	s__Cytobacillus sp000518885	76.8957	171	1533	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_016107705.1	s__Neobacillus cucumis_B	76.8732	123	1533	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_014656545.1	s__Neobacillus sp014656545	76.7434	128	1533	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_001591445.1	s__Neobacillus drentensis	76.6988	114	1533	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_007678255.1	s__Neobacillus sp007678255	76.6519	133	1533	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:01,016] [INFO] GTDB search result was written to GCF_013343715.1_ASM1334371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:01,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:01,022] [INFO] DFAST_QC result json was written to GCF_013343715.1_ASM1334371v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:01,022] [INFO] DFAST_QC completed!
[2024-01-24 13:24:01,022] [INFO] Total running time: 0h1m29s