[2024-01-24 12:14:09,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference
[2024-01-24 12:14:11,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,304] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg580705a7-d74b-4972-829c-d01e6e4d4b4b/GCF_900291985.1_PRJEB24951_genomic.fna.gz | prodigal -d GCF_900291985.1_PRJEB24951_genomic.fna/cds.fna -a GCF_900291985.1_PRJEB24951_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:19,454] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:19,455] [INFO] Task started: HMMsearch
[2024-01-24 12:14:19,455] [INFO] Running command: hmmsearch --tblout GCF_900291985.1_PRJEB24951_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference/reference_markers.hmm GCF_900291985.1_PRJEB24951_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:19,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:19,790] [INFO] Found 6/6 markers.
[2024-01-24 12:14:19,825] [INFO] Query marker FASTA was written to GCF_900291985.1_PRJEB24951_genomic.fna/markers.fasta
[2024-01-24 12:14:19,825] [INFO] Task started: Blastn
[2024-01-24 12:14:19,825] [INFO] Running command: blastn -query GCF_900291985.1_PRJEB24951_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference/reference_markers.fasta -out GCF_900291985.1_PRJEB24951_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:20,447] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:20,451] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:20,451] [INFO] Target genome list was writen to GCF_900291985.1_PRJEB24951_genomic.fna/target_genomes.txt
[2024-01-24 12:14:20,473] [INFO] Task started: fastANI
[2024-01-24 12:14:20,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg580705a7-d74b-4972-829c-d01e6e4d4b4b/GCF_900291985.1_PRJEB24951_genomic.fna.gz --refList GCF_900291985.1_PRJEB24951_genomic.fna/target_genomes.txt --output GCF_900291985.1_PRJEB24951_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:32,886] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:32,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:32,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:32,899] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:32,899] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:32,899] [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
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	80.9689	81	1406	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	80.2332	555	1406	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	80.2228	555	1406	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.8759	85	1406	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	79.7759	508	1406	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_002200865.1	1266064	1266064	type	True	79.6762	490	1406	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	79.6562	491	1406	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.6273	354	1406	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.6189	351	1406	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	78.499	256	1406	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	78.4378	295	1406	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	78.0991	140	1406	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.8895	180	1406	95	below_threshold
Ureibacillus thermosphaericus	strain=DSM 10633	GCA_014202525.1	51173	51173	type	True	77.5485	189	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:32,901] [INFO] DFAST Taxonomy check result was written to GCF_900291985.1_PRJEB24951_genomic.fna/tc_result.tsv
[2024-01-24 12:14:32,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:32,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:32,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference/checkm_data
[2024-01-24 12:14:32,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:32,945] [INFO] Task started: CheckM
[2024-01-24 12:14:32,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900291985.1_PRJEB24951_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900291985.1_PRJEB24951_genomic.fna/checkm_input GCF_900291985.1_PRJEB24951_genomic.fna/checkm_result
[2024-01-24 12:15:04,418] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:04,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:04,442] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:04,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:04,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900291985.1_PRJEB24951_genomic.fna/markers.fasta)
[2024-01-24 12:15:04,443] [INFO] Task started: Blastn
[2024-01-24 12:15:04,443] [INFO] Running command: blastn -query GCF_900291985.1_PRJEB24951_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c02e49-8382-40ea-b2d0-27e17d3eea88/dqc_reference/reference_markers_gtdb.fasta -out GCF_900291985.1_PRJEB24951_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:05,310] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:05,313] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:05,313] [INFO] Target genome list was writen to GCF_900291985.1_PRJEB24951_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:05,330] [INFO] Task started: fastANI
[2024-01-24 12:15:05,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg580705a7-d74b-4972-829c-d01e6e4d4b4b/GCF_900291985.1_PRJEB24951_genomic.fna.gz --refList GCF_900291985.1_PRJEB24951_genomic.fna/target_genomes_gtdb.txt --output GCF_900291985.1_PRJEB24951_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:19,071] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:19,088] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:19,088] [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_900291985.1	s__Ureibacillus timonensis	100.0	1404	1406	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_003351785.1	s__Sporosarcina sp003351785	80.7495	54	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772965.1	s__Ureibacillus massiliensis	80.2439	553	1406	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_900220965.1	s__Ureibacillus acetophenoni	79.7409	509	1406	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_000772945.1	s__Ureibacillus manganicus	79.6728	491	1406	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_005491425.1	s__Ureibacillus sp005491425	79.5033	345	1406	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_003966145.1	s__Ureibacillus telephonicus	79.278	403	1406	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	78.8881	336	1406	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	78.8425	356	1406	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	78.7395	321	1406	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	78.6329	351	1406	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_900217795.1	s__Ureibacillus xyleni	78.6277	347	1406	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	78.4537	293	1406	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_001700315.1	s__Caryophanon tenue	78.0993	137	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Caryophanon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001275675.1	s__Lysinibacillus sp001275675	78.051	195	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396605.1	s__Ureibacillus thermosphaericus	77.5963	186	1406	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.22	98.33	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,090] [INFO] GTDB search result was written to GCF_900291985.1_PRJEB24951_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:19,091] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:19,095] [INFO] DFAST_QC result json was written to GCF_900291985.1_PRJEB24951_genomic.fna/dqc_result.json
[2024-01-24 12:15:19,095] [INFO] DFAST_QC completed!
[2024-01-24 12:15:19,095] [INFO] Total running time: 0h1m9s