[2024-01-24 13:57:56,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,747] [INFO] DQC Reference Directory: /var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference
[2024-01-24 13:57:58,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,124] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a182c50-51f6-428d-9569-bacc390185bd/GCF_002926065.1_ASM292606v1_genomic.fna.gz | prodigal -d GCF_002926065.1_ASM292606v1_genomic.fna/cds.fna -a GCF_002926065.1_ASM292606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:07,711] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:07,711] [INFO] Task started: HMMsearch
[2024-01-24 13:58:07,712] [INFO] Running command: hmmsearch --tblout GCF_002926065.1_ASM292606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference/reference_markers.hmm GCF_002926065.1_ASM292606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:08,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:08,039] [INFO] Found 6/6 markers.
[2024-01-24 13:58:08,085] [INFO] Query marker FASTA was written to GCF_002926065.1_ASM292606v1_genomic.fna/markers.fasta
[2024-01-24 13:58:08,085] [INFO] Task started: Blastn
[2024-01-24 13:58:08,085] [INFO] Running command: blastn -query GCF_002926065.1_ASM292606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference/reference_markers.fasta -out GCF_002926065.1_ASM292606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,683] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,686] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:08,686] [INFO] Target genome list was writen to GCF_002926065.1_ASM292606v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:08,752] [INFO] Task started: fastANI
[2024-01-24 13:58:08,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a182c50-51f6-428d-9569-bacc390185bd/GCF_002926065.1_ASM292606v1_genomic.fna.gz --refList GCF_002926065.1_ASM292606v1_genomic.fna/target_genomes.txt --output GCF_002926065.1_ASM292606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:24,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:24,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:24,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:24,299] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:24,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:24,299] [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
Jeotgalibacillus proteolyticus	strain=22-7	GCA_002926065.1	2082395	2082395	type	True	100.0	1388	1403	95	conclusive
Bacillus vallismortis	strain=DSM 11031	GCA_004116955.1	72361	72361	type	True	79.1375	59	1403	95	below_threshold
Jeotgalibacillus campisalis	strain=SF-57	GCA_000829515.1	220754	220754	type	True	78.9434	386	1403	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	78.693	56	1403	95	below_threshold
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	78.6086	50	1403	95	below_threshold
Jeotgalibacillus malaysiensis	strain=D5	GCA_000818095.1	1508404	1508404	type	True	78.0033	221	1403	95	below_threshold
Jeotgalibacillus alimentarius	strain=YKJ-13	GCA_000829445.1	135826	135826	type	True	77.9513	185	1403	95	below_threshold
Jeotgalibacillus terrae	strain=DSM 22174	GCA_016908195.1	587735	587735	type	True	77.6151	193	1403	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	77.5322	57	1403	95	below_threshold
Mesobacillus foraminis	strain=CV53	GCA_013618915.1	279826	279826	type	True	77.5058	53	1403	95	below_threshold
Jeotgalibacillus salarius	strain=ASL-1	GCA_004405125.1	546023	546023	type	True	77.4824	189	1403	95	below_threshold
Jeotgalibacillus aurantiacus	strain=T12	GCA_020595125.1	2763266	2763266	type	True	77.4678	220	1403	95	below_threshold
Peribacillus alkalitolerans	strain=KCTC 33631	GCA_010882125.1	1550385	1550385	type	True	76.4478	50	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:24,301] [INFO] DFAST Taxonomy check result was written to GCF_002926065.1_ASM292606v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:24,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:24,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:24,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference/checkm_data
[2024-01-24 13:58:24,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:24,346] [INFO] Task started: CheckM
[2024-01-24 13:58:24,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002926065.1_ASM292606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002926065.1_ASM292606v1_genomic.fna/checkm_input GCF_002926065.1_ASM292606v1_genomic.fna/checkm_result
[2024-01-24 13:58:58,344] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:58,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:58,364] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:58,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:58,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002926065.1_ASM292606v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:58,365] [INFO] Task started: Blastn
[2024-01-24 13:58:58,365] [INFO] Running command: blastn -query GCF_002926065.1_ASM292606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf633de84-b23a-44e9-ba86-563e0d1d345a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002926065.1_ASM292606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:59,199] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:59,203] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:59,203] [INFO] Target genome list was writen to GCF_002926065.1_ASM292606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:59,292] [INFO] Task started: fastANI
[2024-01-24 13:58:59,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a182c50-51f6-428d-9569-bacc390185bd/GCF_002926065.1_ASM292606v1_genomic.fna.gz --refList GCF_002926065.1_ASM292606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002926065.1_ASM292606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:15,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:15,055] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:15,055] [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_002926065.1	s__Jeotgalibacillus proteolyticus	100.0	1384	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004358665.1	s__Jeotgalibacillus sp004358665	79.2533	437	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829515.1	s__Jeotgalibacillus campisalis	78.9247	385	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116955.1	s__Bacillus vallismortis	78.9191	57	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
GCF_000818095.1	s__Jeotgalibacillus malaysiensis	78.0718	222	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829445.1	s__Jeotgalibacillus alimentarius	78.0243	180	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908195.1	s__Jeotgalibacillus terrae	77.6478	191	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004405105.1	s__Jeotgalibacillus sp004405105	77.6285	225	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004405125.1	s__Jeotgalibacillus salarius	77.4824	189	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180415.1	s__Bacillus_BM vietnamensis_B	77.4299	70	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424685.1	s__Mesobacillus boroniphilus_A	76.9645	51	1403	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_001591825.1	s__Rossellomorea vietnamensis	76.8391	63	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	97.54	97.34	0.88	0.87	6	-
GCF_004340465.1	s__Bacillus_AZ foraminis	76.7267	51	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	97.82	96.47	0.93	0.88	4	-
GCF_002153395.1	s__Bacillus subtilis_G	76.5343	52	1403	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:15,057] [INFO] GTDB search result was written to GCF_002926065.1_ASM292606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:15,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:15,061] [INFO] DFAST_QC result json was written to GCF_002926065.1_ASM292606v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:15,061] [INFO] DFAST_QC completed!
[2024-01-24 13:59:15,061] [INFO] Total running time: 0h1m18s