[2024-01-25 19:33:21,058] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:21,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:21,059] [INFO] DQC Reference Directory: /var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference
[2024-01-25 19:33:22,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,220] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,220] [INFO] Running command: gunzip -c /var/lib/cwl/stgfac7f555-5ade-442b-8600-1933a40d0b9f/GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/cds.fna -a GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:28,812] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:28,813] [INFO] Task started: HMMsearch
[2024-01-25 19:33:28,813] [INFO] Running command: hmmsearch --tblout GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference/reference_markers.hmm GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:29,051] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:29,052] [INFO] Found 6/6 markers.
[2024-01-25 19:33:29,084] [INFO] Query marker FASTA was written to GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:33:29,084] [INFO] Task started: Blastn
[2024-01-25 19:33:29,084] [INFO] Running command: blastn -query GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference/reference_markers.fasta -out GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:29,660] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:29,663] [INFO] Selected 12 target genomes.
[2024-01-25 19:33:29,663] [INFO] Target genome list was writen to GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:33:29,668] [INFO] Task started: fastANI
[2024-01-25 19:33:29,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac7f555-5ade-442b-8600-1933a40d0b9f/GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna.gz --refList GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:38,236] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:38,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:38,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:38,244] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:38,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:38,244] [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
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	100.0	1301	1303	95	conclusive
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	82.8445	891	1303	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_002200865.1	1266064	1266064	type	True	82.8351	892	1303	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	79.344	474	1303	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.3438	474	1303	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.6602	359	1303	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	78.5301	302	1303	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.042	191	1303	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	77.4828	179	1303	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	77.3378	119	1303	95	below_threshold
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	77.3142	119	1303	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.1662	86	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:38,245] [INFO] DFAST Taxonomy check result was written to GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:33:38,246] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:38,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:38,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference/checkm_data
[2024-01-25 19:33:38,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:38,286] [INFO] Task started: CheckM
[2024-01-25 19:33:38,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/checkm_input GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:34:02,027] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:02,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:02,046] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:02,047] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:02,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:34:02,048] [INFO] Task started: Blastn
[2024-01-25 19:34:02,048] [INFO] Running command: blastn -query GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge435300e-3ec1-47e1-a35b-e650ed99fa95/dqc_reference/reference_markers_gtdb.fasta -out GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:02,787] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:02,790] [INFO] Selected 13 target genomes.
[2024-01-25 19:34:02,790] [INFO] Target genome list was writen to GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:02,796] [INFO] Task started: fastANI
[2024-01-25 19:34:02,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgfac7f555-5ade-442b-8600-1933a40d0b9f/GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna.gz --refList GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:12,476] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:12,484] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:34:12,484] [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_900220965.1	s__Ureibacillus acetophenoni	100.0	1301	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000772945.1	s__Ureibacillus manganicus	82.8603	889	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900291985.1	s__Ureibacillus timonensis	79.5976	514	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772965.1	s__Ureibacillus massiliensis	79.3543	473	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003628435.1	s__Ureibacillus endophyticus	78.8816	344	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900217795.1	s__Ureibacillus xyleni	78.8104	362	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	78.796	336	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977595.1	s__Ureibacillus antri	78.6469	346	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	-
GCF_016908465.1	s__Ureibacillus composti	78.5935	355	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836845.1	s__Ureibacillus sp014836845	78.4947	342	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143955.1	s__Kurthia zopfii	77.3378	119	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	-
GCF_000311725.1	s__Robertmurraya massiliosenegalensis	76.3999	64	1303	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	-
GCF_007679095.1	s__DE0126 sp007679095	76.332	64	1303	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:12,485] [INFO] GTDB search result was written to GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:12,486] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:12,489] [INFO] DFAST_QC result json was written to GCF_900220965.1_IMG-taxon_2740891860_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:34:12,489] [INFO] DFAST_QC completed!
[2024-01-25 19:34:12,489] [INFO] Total running time: 0h0m51s