[2024-01-24 13:17:05,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,711] [INFO] DQC Reference Directory: /var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference
[2024-01-24 13:17:07,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:07,085] [INFO] Task started: Prodigal
[2024-01-24 13:17:07,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg870fbc9e-935b-431d-9709-2c636151c32c/GCF_001591665.1_ASM159166v1_genomic.fna.gz | prodigal -d GCF_001591665.1_ASM159166v1_genomic.fna/cds.fna -a GCF_001591665.1_ASM159166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:18,448] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:18,449] [INFO] Task started: HMMsearch
[2024-01-24 13:17:18,449] [INFO] Running command: hmmsearch --tblout GCF_001591665.1_ASM159166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference/reference_markers.hmm GCF_001591665.1_ASM159166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:18,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:18,801] [INFO] Found 6/6 markers.
[2024-01-24 13:17:18,844] [INFO] Query marker FASTA was written to GCF_001591665.1_ASM159166v1_genomic.fna/markers.fasta
[2024-01-24 13:17:18,845] [INFO] Task started: Blastn
[2024-01-24 13:17:18,845] [INFO] Running command: blastn -query GCF_001591665.1_ASM159166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference/reference_markers.fasta -out GCF_001591665.1_ASM159166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:19,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:19,483] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:19,483] [INFO] Target genome list was writen to GCF_001591665.1_ASM159166v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:19,489] [INFO] Task started: fastANI
[2024-01-24 13:17:19,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg870fbc9e-935b-431d-9709-2c636151c32c/GCF_001591665.1_ASM159166v1_genomic.fna.gz --refList GCF_001591665.1_ASM159166v1_genomic.fna/target_genomes.txt --output GCF_001591665.1_ASM159166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:35,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:35,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:35,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:35,451] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:35,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:35,452] [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 soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	100.0	1749	1756	95	conclusive
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	99.9971	1756	1756	95	conclusive
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	82.7418	953	1756	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	82.7409	957	1756	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	81.7767	888	1756	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	81.7403	831	1756	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	80.8813	830	1756	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	80.1345	754	1756	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	80.0553	787	1756	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.3882	469	1756	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.2671	437	1756	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.7581	263	1756	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.6006	174	1756	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.8651	84	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:35,453] [INFO] DFAST Taxonomy check result was written to GCF_001591665.1_ASM159166v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:35,454] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:35,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:35,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference/checkm_data
[2024-01-24 13:17:35,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:35,514] [INFO] Task started: CheckM
[2024-01-24 13:17:35,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591665.1_ASM159166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591665.1_ASM159166v1_genomic.fna/checkm_input GCF_001591665.1_ASM159166v1_genomic.fna/checkm_result
[2024-01-24 13:18:14,017] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:14,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:14,041] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:14,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:14,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591665.1_ASM159166v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:14,042] [INFO] Task started: Blastn
[2024-01-24 13:18:14,042] [INFO] Running command: blastn -query GCF_001591665.1_ASM159166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18c4311-10ac-4294-818f-c480577b5f04/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591665.1_ASM159166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:14,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:14,832] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:14,832] [INFO] Target genome list was writen to GCF_001591665.1_ASM159166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:14,855] [INFO] Task started: fastANI
[2024-01-24 13:18:14,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg870fbc9e-935b-431d-9709-2c636151c32c/GCF_001591665.1_ASM159166v1_genomic.fna.gz --refList GCF_001591665.1_ASM159166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591665.1_ASM159166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:29,988] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:30,006] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:30,007] [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_001591665.1	s__Neobacillus soli	100.0	1749	1756	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	conclusive
GCF_001591805.1	s__Neobacillus novalis	82.7565	951	1756	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_001026695.1	s__Neobacillus vireti	81.781	888	1756	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_000307875.1	s__Neobacillus bataviensis	80.8817	830	1756	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_900177675.1	s__Neobacillus sp900177675	80.3984	853	1756	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_018613065.1	s__Neobacillus sp018613065	80.3559	792	1756	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_005154805.1	s__Neobacillus sp005154805	80.1902	821	1756	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	80.1229	756	1756	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_000686805.1	s__Neobacillus sp000686805	79.9432	724	1756	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_011250555.1	s__Neobacillus sp011250555	79.88	681	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002559145.1	s__Neobacillus sp002559145	79.853	711	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.43	95.43	0.81	0.81	2	-
GCF_007678255.1	s__Neobacillus sp007678255	79.7652	703	1756	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	79.6225	771	1756	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 13:18:30,008] [INFO] GTDB search result was written to GCF_001591665.1_ASM159166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:30,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:30,014] [INFO] DFAST_QC result json was written to GCF_001591665.1_ASM159166v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:30,014] [INFO] DFAST_QC completed!
[2024-01-24 13:18:30,014] [INFO] Total running time: 0h1m24s