[2024-01-24 13:50:26,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference
[2024-01-24 13:50:27,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,671] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b968d1e-629d-4c0f-a6e2-fd39aca8d9ab/GCF_030813005.1_ASM3081300v1_genomic.fna.gz | prodigal -d GCF_030813005.1_ASM3081300v1_genomic.fna/cds.fna -a GCF_030813005.1_ASM3081300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:37,101] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:37,102] [INFO] Task started: HMMsearch
[2024-01-24 13:50:37,102] [INFO] Running command: hmmsearch --tblout GCF_030813005.1_ASM3081300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference/reference_markers.hmm GCF_030813005.1_ASM3081300v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:37,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:37,393] [INFO] Found 6/6 markers.
[2024-01-24 13:50:37,433] [INFO] Query marker FASTA was written to GCF_030813005.1_ASM3081300v1_genomic.fna/markers.fasta
[2024-01-24 13:50:37,434] [INFO] Task started: Blastn
[2024-01-24 13:50:37,434] [INFO] Running command: blastn -query GCF_030813005.1_ASM3081300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference/reference_markers.fasta -out GCF_030813005.1_ASM3081300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,013] [INFO] Selected 25 target genomes.
[2024-01-24 13:50:38,013] [INFO] Target genome list was writen to GCF_030813005.1_ASM3081300v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:38,099] [INFO] Task started: fastANI
[2024-01-24 13:50:38,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b968d1e-629d-4c0f-a6e2-fd39aca8d9ab/GCF_030813005.1_ASM3081300v1_genomic.fna.gz --refList GCF_030813005.1_ASM3081300v1_genomic.fna/target_genomes.txt --output GCF_030813005.1_ASM3081300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:54,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:54,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:54,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:54,690] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:54,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:54,690] [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
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	79.6053	97	1406	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	78.9764	328	1406	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	78.9495	330	1406	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	78.8581	313	1406	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	78.3016	55	1406	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	78.0803	224	1406	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	77.8838	116	1406	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.838	72	1406	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.8094	168	1406	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.7611	116	1406	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	77.5491	72	1406	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.3979	82	1406	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.3084	121	1406	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	77.2842	98	1406	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.2659	77	1406	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.2006	115	1406	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.1221	123	1406	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.0805	64	1406	95	below_threshold
Niallia taxi	strain=M5HDSG1-1	GCA_004005475.1	2499688	2499688	type	True	77.0386	85	1406	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.9726	99	1406	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.8498	70	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:54,692] [INFO] DFAST Taxonomy check result was written to GCF_030813005.1_ASM3081300v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:54,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:54,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:54,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference/checkm_data
[2024-01-24 13:50:54,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:54,738] [INFO] Task started: CheckM
[2024-01-24 13:50:54,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813005.1_ASM3081300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813005.1_ASM3081300v1_genomic.fna/checkm_input GCF_030813005.1_ASM3081300v1_genomic.fna/checkm_result
[2024-01-24 13:51:28,253] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:28,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:28,277] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:28,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:28,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813005.1_ASM3081300v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:28,278] [INFO] Task started: Blastn
[2024-01-24 13:51:28,279] [INFO] Running command: blastn -query GCF_030813005.1_ASM3081300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f90ce2a-7ffd-45b1-aca6-a4039d29dda1/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813005.1_ASM3081300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:29,030] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:29,035] [INFO] Selected 26 target genomes.
[2024-01-24 13:51:29,035] [INFO] Target genome list was writen to GCF_030813005.1_ASM3081300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:29,255] [INFO] Task started: fastANI
[2024-01-24 13:51:29,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b968d1e-629d-4c0f-a6e2-fd39aca8d9ab/GCF_030813005.1_ASM3081300v1_genomic.fna.gz --refList GCF_030813005.1_ASM3081300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813005.1_ASM3081300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:49,377] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:49,410] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:49,411] [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
GCA_002480735.1	s__Robertmurraya sp002480735	98.3458	956	1406	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	conclusive
GCF_005116465.1	s__Robertmurraya kyonggiensis	79.1245	343	1406	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_005280205.1	s__Robertmurraya yapensis	78.9632	329	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000311725.1	s__Robertmurraya massiliosenegalensis	78.8581	313	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009917645.1	s__Robertmurraya sp009917645	78.6778	156	1406	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_018343665.1	s__Cytobacillus sp018343665	77.9379	148	1406	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_902168435.1	s__Bacillus_BU marasmi	77.8892	115	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019645.1	s__Litchfieldia alkalitelluris	77.8865	74	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274725.1	s__Cytobacillus globisporus	77.8438	124	1406	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_000724485.1	s__Bacillus_Z methanolicus_A	77.8159	101	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007995155.1	s__Cytobacillus dafuensis	77.8094	168	1406	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_900199725.1	s__Cytobacillus massiliigabonensis	77.7032	170	1406	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_002835805.1	s__Niallia nealsonii	77.5491	72	1406	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	-
GCF_900103525.1	s__Neobacillus sp900103525	77.5097	128	1406	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	77.4665	128	1406	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_000686805.1	s__Neobacillus sp000686805	77.439	115	1406	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_007273535.1	s__Niallia circulans_B	77.4361	85	1406	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	-
GCF_014217835.1	s__Metabacillus litoralis_A	77.367	85	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_900104555.1	s__Litchfieldia salsa	77.2659	77	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409995.1	s__Neobacillus niacini_B	77.2185	126	1406	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	77.164	130	1406	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	77.1221	123	1406	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	77.0427	126	1406	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	76.9903	123	1406	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_011008855.1	s__Bacillus_BT aquiflavi	76.9898	100	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BT	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:49,413] [INFO] GTDB search result was written to GCF_030813005.1_ASM3081300v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:49,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:49,418] [INFO] DFAST_QC result json was written to GCF_030813005.1_ASM3081300v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:49,419] [INFO] DFAST_QC completed!
[2024-01-24 13:51:49,419] [INFO] Total running time: 0h1m23s