[2024-01-24 13:57:55,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference
[2024-01-24 13:57:57,298] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,299] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,300] [INFO] Running command: gunzip -c /var/lib/cwl/stge7987035-4cd5-4085-95ea-bb844da478af/GCF_001591445.1_ASM159144v1_genomic.fna.gz | prodigal -d GCF_001591445.1_ASM159144v1_genomic.fna/cds.fna -a GCF_001591445.1_ASM159144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:07,843] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:07,843] [INFO] Task started: HMMsearch
[2024-01-24 13:58:07,844] [INFO] Running command: hmmsearch --tblout GCF_001591445.1_ASM159144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference/reference_markers.hmm GCF_001591445.1_ASM159144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:08,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:08,261] [INFO] Found 6/6 markers.
[2024-01-24 13:58:08,307] [INFO] Query marker FASTA was written to GCF_001591445.1_ASM159144v1_genomic.fna/markers.fasta
[2024-01-24 13:58:08,307] [INFO] Task started: Blastn
[2024-01-24 13:58:08,307] [INFO] Running command: blastn -query GCF_001591445.1_ASM159144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference/reference_markers.fasta -out GCF_001591445.1_ASM159144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,965] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,968] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:08,968] [INFO] Target genome list was writen to GCF_001591445.1_ASM159144v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:08,972] [INFO] Task started: fastANI
[2024-01-24 13:58:08,972] [INFO] Running command: fastANI --query /var/lib/cwl/stge7987035-4cd5-4085-95ea-bb844da478af/GCF_001591445.1_ASM159144v1_genomic.fna.gz --refList GCF_001591445.1_ASM159144v1_genomic.fna/target_genomes.txt --output GCF_001591445.1_ASM159144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:22,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:22,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:22,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:22,951] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:22,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:22,951] [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 drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	100.0	1643	1650	95	conclusive
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	99.9989	1650	1650	95	conclusive
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	80.147	770	1650	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	80.1155	756	1650	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	79.8215	603	1650	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	79.5888	630	1650	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	79.5758	597	1650	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	79.5541	640	1650	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	79.516	568	1650	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.8558	460	1650	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.0242	378	1650	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.2425	159	1650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,953] [INFO] DFAST Taxonomy check result was written to GCF_001591445.1_ASM159144v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:22,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:22,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:22,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference/checkm_data
[2024-01-24 13:58:22,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:23,017] [INFO] Task started: CheckM
[2024-01-24 13:58:23,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591445.1_ASM159144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591445.1_ASM159144v1_genomic.fna/checkm_input GCF_001591445.1_ASM159144v1_genomic.fna/checkm_result
[2024-01-24 13:59:02,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:02,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:02,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:02,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591445.1_ASM159144v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:02,035] [INFO] Task started: Blastn
[2024-01-24 13:59:02,035] [INFO] Running command: blastn -query GCF_001591445.1_ASM159144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d67bf9-e232-4142-9800-7b910f555350/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591445.1_ASM159144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:02,908] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:02,911] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:02,912] [INFO] Target genome list was writen to GCF_001591445.1_ASM159144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:02,919] [INFO] Task started: fastANI
[2024-01-24 13:59:02,919] [INFO] Running command: fastANI --query /var/lib/cwl/stge7987035-4cd5-4085-95ea-bb844da478af/GCF_001591445.1_ASM159144v1_genomic.fna.gz --refList GCF_001591445.1_ASM159144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591445.1_ASM159144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:14,741] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:14,753] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:14,754] [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_001591445.1	s__Neobacillus drentensis	100.0	1643	1650	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_002559145.1	s__Neobacillus sp002559145	92.9144	1215	1650	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_900177675.1	s__Neobacillus sp900177675	85.9003	1186	1650	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	85.8541	1083	1650	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_000686805.1	s__Neobacillus sp000686805	83.1063	1072	1650	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	83.0043	1085	1650	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_002567005.1	s__Neobacillus sp002567005	82.4366	999	1650	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_000307875.1	s__Neobacillus bataviensis	79.7911	607	1650	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 13:59:14,755] [INFO] GTDB search result was written to GCF_001591445.1_ASM159144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:14,756] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:14,762] [INFO] DFAST_QC result json was written to GCF_001591445.1_ASM159144v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:14,762] [INFO] DFAST_QC completed!
[2024-01-24 13:59:14,762] [INFO] Total running time: 0h1m19s