[2024-01-24 13:25:30,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,494] [INFO] DQC Reference Directory: /var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference
[2024-01-24 13:25:31,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,904] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg67c1199c-2d84-4725-84ca-1c9185c7c4c8/GCF_002200865.1_ASM220086v1_genomic.fna.gz | prodigal -d GCF_002200865.1_ASM220086v1_genomic.fna/cds.fna -a GCF_002200865.1_ASM220086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:39,451] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:39,451] [INFO] Task started: HMMsearch
[2024-01-24 13:25:39,451] [INFO] Running command: hmmsearch --tblout GCF_002200865.1_ASM220086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference/reference_markers.hmm GCF_002200865.1_ASM220086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:39,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:39,789] [INFO] Found 6/6 markers.
[2024-01-24 13:25:39,826] [INFO] Query marker FASTA was written to GCF_002200865.1_ASM220086v1_genomic.fna/markers.fasta
[2024-01-24 13:25:39,827] [INFO] Task started: Blastn
[2024-01-24 13:25:39,827] [INFO] Running command: blastn -query GCF_002200865.1_ASM220086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference/reference_markers.fasta -out GCF_002200865.1_ASM220086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:40,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:40,449] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:40,450] [INFO] Target genome list was writen to GCF_002200865.1_ASM220086v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:40,460] [INFO] Task started: fastANI
[2024-01-24 13:25:40,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c1199c-2d84-4725-84ca-1c9185c7c4c8/GCF_002200865.1_ASM220086v1_genomic.fna.gz --refList GCF_002200865.1_ASM220086v1_genomic.fna/target_genomes.txt --output GCF_002200865.1_ASM220086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:49,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:49,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:49,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:50,005] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:50,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:50,006] [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 manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	100.0	1316	1317	95	conclusive
Ureibacillus manganicus	strain=DSM 26584	GCA_002200865.1	1266064	1266064	type	True	100.0	1316	1317	95	conclusive
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	82.9369	876	1317	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.4502	451	1317	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	79.4406	451	1317	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.4502	355	1317	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.4132	355	1317	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.1488	187	1317	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	76.4802	58	1317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:50,007] [INFO] DFAST Taxonomy check result was written to GCF_002200865.1_ASM220086v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:50,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:50,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:50,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference/checkm_data
[2024-01-24 13:25:50,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:50,050] [INFO] Task started: CheckM
[2024-01-24 13:25:50,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002200865.1_ASM220086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002200865.1_ASM220086v1_genomic.fna/checkm_input GCF_002200865.1_ASM220086v1_genomic.fna/checkm_result
[2024-01-24 13:26:18,454] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:18,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:18,478] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:18,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:18,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002200865.1_ASM220086v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:18,480] [INFO] Task started: Blastn
[2024-01-24 13:26:18,480] [INFO] Running command: blastn -query GCF_002200865.1_ASM220086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1075b45-7255-4e0d-84c4-155b2dfb8531/dqc_reference/reference_markers_gtdb.fasta -out GCF_002200865.1_ASM220086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:19,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:19,260] [INFO] Selected 16 target genomes.
[2024-01-24 13:26:19,260] [INFO] Target genome list was writen to GCF_002200865.1_ASM220086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:19,276] [INFO] Task started: fastANI
[2024-01-24 13:26:19,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c1199c-2d84-4725-84ca-1c9185c7c4c8/GCF_002200865.1_ASM220086v1_genomic.fna.gz --refList GCF_002200865.1_ASM220086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002200865.1_ASM220086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:29,853] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:29,876] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:29,877] [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_000772945.1	s__Ureibacillus manganicus	100.0	1316	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900220965.1	s__Ureibacillus acetophenoni	82.9159	879	1317	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_900291985.1	s__Ureibacillus timonensis	79.5992	499	1317	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	79.4406	451	1317	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_003977595.1	s__Ureibacillus antri	78.9005	338	1317	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_003966145.1	s__Ureibacillus telephonicus	78.8606	329	1317	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_014836845.1	s__Ureibacillus sp014836845	78.6962	328	1317	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	78.6924	342	1317	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_003628435.1	s__Ureibacillus endophyticus	78.6771	346	1317	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_003217295.1	s__Ureibacillus chungkukjangi	78.5849	315	1317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003711845.1	s__Ureibacillus halotolerans	78.4526	319	1317	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_016908465.1	s__Ureibacillus composti	78.4171	354	1317	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_000311725.1	s__Robertmurraya massiliosenegalensis	76.4802	58	1317	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:29,879] [INFO] GTDB search result was written to GCF_002200865.1_ASM220086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:29,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:29,884] [INFO] DFAST_QC result json was written to GCF_002200865.1_ASM220086v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:29,885] [INFO] DFAST_QC completed!
[2024-01-24 13:26:29,885] [INFO] Total running time: 0h0m59s