[2024-01-25 17:54:35,850] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference
[2024-01-25 17:54:37,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:37,040] [INFO] Task started: Prodigal
[2024-01-25 17:54:37,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg24854a95-3754-47dd-841a-db19a0938e0f/GCF_030814045.1_ASM3081404v1_genomic.fna.gz | prodigal -d GCF_030814045.1_ASM3081404v1_genomic.fna/cds.fna -a GCF_030814045.1_ASM3081404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:45,342] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:45,342] [INFO] Task started: HMMsearch
[2024-01-25 17:54:45,342] [INFO] Running command: hmmsearch --tblout GCF_030814045.1_ASM3081404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference/reference_markers.hmm GCF_030814045.1_ASM3081404v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:45,670] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:45,671] [INFO] Found 6/6 markers.
[2024-01-25 17:54:45,707] [INFO] Query marker FASTA was written to GCF_030814045.1_ASM3081404v1_genomic.fna/markers.fasta
[2024-01-25 17:54:45,708] [INFO] Task started: Blastn
[2024-01-25 17:54:45,708] [INFO] Running command: blastn -query GCF_030814045.1_ASM3081404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference/reference_markers.fasta -out GCF_030814045.1_ASM3081404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:46,263] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:46,266] [INFO] Selected 14 target genomes.
[2024-01-25 17:54:46,267] [INFO] Target genome list was writen to GCF_030814045.1_ASM3081404v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:46,270] [INFO] Task started: fastANI
[2024-01-25 17:54:46,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg24854a95-3754-47dd-841a-db19a0938e0f/GCF_030814045.1_ASM3081404v1_genomic.fna.gz --refList GCF_030814045.1_ASM3081404v1_genomic.fna/target_genomes.txt --output GCF_030814045.1_ASM3081404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:59,615] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:59,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:59,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:59,625] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:59,625] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:59,626] [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
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	99.999	1481	1486	95	conclusive
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	84.8599	1155	1486	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	82.954	1046	1486	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	81.2597	884	1486	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	77.1244	104	1486	95	below_threshold
Bacillus niameyensis	strain=SIT3	GCA_001375535.1	1522308	1522308	type	True	77.0892	216	1486	95	below_threshold
Peribacillus loiseleuriae	strain=FJAT-27997	GCA_001183985.1	1679170	1679170	type	True	76.9584	88	1486	95	below_threshold
Siminovitchia thermophila	strain=DSM 105453	GCA_016909185.1	1245522	1245522	type	True	76.8013	90	1486	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.5661	87	1486	95	below_threshold
Bacillus ectoiniformans	strain=DSM 28970	GCA_016908875.1	1494429	1494429	type	True	76.4907	51	1486	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	76.2314	85	1486	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.1143	84	1486	95	below_threshold
Jeotgalibacillus soli	strain=P9	GCA_000829435.1	889306	889306	type	True	75.916	66	1486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:59,627] [INFO] DFAST Taxonomy check result was written to GCF_030814045.1_ASM3081404v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:59,627] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:59,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:59,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference/checkm_data
[2024-01-25 17:54:59,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:59,675] [INFO] Task started: CheckM
[2024-01-25 17:54:59,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814045.1_ASM3081404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814045.1_ASM3081404v1_genomic.fna/checkm_input GCF_030814045.1_ASM3081404v1_genomic.fna/checkm_result
[2024-01-25 17:55:27,732] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:27,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:27,751] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:27,751] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:27,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814045.1_ASM3081404v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:27,752] [INFO] Task started: Blastn
[2024-01-25 17:55:27,752] [INFO] Running command: blastn -query GCF_030814045.1_ASM3081404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg478a0630-f03d-45d0-a644-99a7671a5725/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814045.1_ASM3081404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:28,510] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:28,514] [INFO] Selected 19 target genomes.
[2024-01-25 17:55:28,514] [INFO] Target genome list was writen to GCF_030814045.1_ASM3081404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:28,529] [INFO] Task started: fastANI
[2024-01-25 17:55:28,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg24854a95-3754-47dd-841a-db19a0938e0f/GCF_030814045.1_ASM3081404v1_genomic.fna.gz --refList GCF_030814045.1_ASM3081404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814045.1_ASM3081404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:44,208] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:44,219] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:55:44,220] [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_018343695.1	s__FJAT-49711 sp018343695	84.8478	1156	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343625.1	s__FJAT-49711 sp018343625	82.9503	1046	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343715.1	s__FJAT-49711 sp018343715	81.2915	953	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343525.1	s__FJAT-49754 sp018343525	78.325	321	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49754	95.0	98.88	98.76	0.94	0.94	3	-
GCF_007679095.1	s__DE0126 sp007679095	77.844	216	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343515.1	s__Bacillus_AH sp018343515	77.5144	203	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756695.1	s__Heyndrickxia sporothermodurans	77.0992	108	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_001375535.1	s__Lederbergia niameyensis	77.0891	215	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008764245.1	s__Lederbergia ruris	76.9674	169	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	98.48	98.48	0.86	0.86	2	-
GCF_001183985.1	s__Peribacillus loiseleuriae	76.931	89	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909185.1	s__Siminovitchia thermophila	76.8005	89	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	99.46	99.46	0.95	0.95	2	-
GCF_013409995.1	s__Neobacillus niacini_B	76.7581	91	1486	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_014837155.1	s__Litchfieldia sp014837155	76.584	79	1486	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_016908875.1	s__Bacillus_BX ectoiniformans	76.4907	51	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_BX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710145.1	s__Bacillus_BD endozanthoxylicus	76.2926	82	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835735.1	s__Cytobacillus horneckiae	76.2524	84	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_001757995.1	s__Bacillus_A mycoides_B	76.1107	69	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.94	99.86	0.98	0.98	4	-
GCF_000829435.1	s__Jeotgalibacillus soli	75.9752	67	1486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:44,221] [INFO] GTDB search result was written to GCF_030814045.1_ASM3081404v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:44,222] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:44,225] [INFO] DFAST_QC result json was written to GCF_030814045.1_ASM3081404v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:44,225] [INFO] DFAST_QC completed!
[2024-01-25 17:55:44,225] [INFO] Total running time: 0h1m8s