[2024-01-24 13:40:30,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference
[2024-01-24 13:40:32,138] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:32,139] [INFO] Task started: Prodigal
[2024-01-24 13:40:32,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg925fbf4d-a3b1-44ba-bf4c-2aa7d61430fb/GCF_017873565.1_ASM1787356v1_genomic.fna.gz | prodigal -d GCF_017873565.1_ASM1787356v1_genomic.fna/cds.fna -a GCF_017873565.1_ASM1787356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,339] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,339] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,339] [INFO] Running command: hmmsearch --tblout GCF_017873565.1_ASM1787356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference/reference_markers.hmm GCF_017873565.1_ASM1787356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:42,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:42,673] [INFO] Found 6/6 markers.
[2024-01-24 13:40:42,713] [INFO] Query marker FASTA was written to GCF_017873565.1_ASM1787356v1_genomic.fna/markers.fasta
[2024-01-24 13:40:42,714] [INFO] Task started: Blastn
[2024-01-24 13:40:42,714] [INFO] Running command: blastn -query GCF_017873565.1_ASM1787356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference/reference_markers.fasta -out GCF_017873565.1_ASM1787356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:43,312] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:43,315] [INFO] Selected 36 target genomes.
[2024-01-24 13:40:43,316] [INFO] Target genome list was writen to GCF_017873565.1_ASM1787356v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:43,338] [INFO] Task started: fastANI
[2024-01-24 13:40:43,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg925fbf4d-a3b1-44ba-bf4c-2aa7d61430fb/GCF_017873565.1_ASM1787356v1_genomic.fna.gz --refList GCF_017873565.1_ASM1787356v1_genomic.fna/target_genomes.txt --output GCF_017873565.1_ASM1787356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:07,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:07,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:07,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:07,169] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:07,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:07,170] [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
Lederbergia galactosidilytica	strain=DSM 15595	GCA_017873565.1	217031	217031	type	True	100.0	1561	1566	95	conclusive
Bacillus niameyensis	strain=SIT3	GCA_001375535.1	1522308	1522308	type	True	77.3507	297	1566	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.169	76	1566	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.9731	187	1566	95	below_threshold
Lederbergia lenta	strain=NCTC4824	GCA_900478165.1	1467	1467	type	True	76.9035	181	1566	95	below_threshold
Lederbergia lenta	strain=NBRC 16444	GCA_001591545.1	1467	1467	type	True	76.8577	179	1566	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	76.7822	96	1566	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.6578	96	1566	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.5859	56	1566	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	76.5273	87	1566	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	76.3203	64	1566	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	76.2718	75	1566	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.2628	77	1566	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	75.8473	60	1566	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	75.7823	97	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:07,171] [INFO] DFAST Taxonomy check result was written to GCF_017873565.1_ASM1787356v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:07,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:07,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:07,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference/checkm_data
[2024-01-24 13:41:07,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:07,228] [INFO] Task started: CheckM
[2024-01-24 13:41:07,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873565.1_ASM1787356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873565.1_ASM1787356v1_genomic.fna/checkm_input GCF_017873565.1_ASM1787356v1_genomic.fna/checkm_result
[2024-01-24 13:41:42,830] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:42,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:42,863] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:42,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:42,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873565.1_ASM1787356v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:42,864] [INFO] Task started: Blastn
[2024-01-24 13:41:42,864] [INFO] Running command: blastn -query GCF_017873565.1_ASM1787356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f2ead65-b494-4ea1-bdef-1a4fc5ae1919/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873565.1_ASM1787356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:43,727] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:43,731] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:43,731] [INFO] Target genome list was writen to GCF_017873565.1_ASM1787356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:43,760] [INFO] Task started: fastANI
[2024-01-24 13:41:43,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg925fbf4d-a3b1-44ba-bf4c-2aa7d61430fb/GCF_017873565.1_ASM1787356v1_genomic.fna.gz --refList GCF_017873565.1_ASM1787356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873565.1_ASM1787356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:01,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:01,818] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:01,818] [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_017873565.1	s__Lederbergia galactosidilytica	100.0	1561	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	99.35	99.18	0.94	0.93	4	conclusive
GCF_008764245.1	s__Lederbergia ruris	84.1238	987	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	98.48	98.48	0.86	0.86	2	-
GCF_017355205.1	s__Lederbergia sp017355205	82.2386	966	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	95.07	95.07	0.86	0.86	2	-
GCF_001375535.1	s__Lederbergia niameyensis	77.3954	290	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	77.169	76	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_007679095.1	s__DE0126 sp007679095	76.9834	161	1566	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	-
GCF_001591545.1	s__Bacillus_AH lentus	76.8692	178	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017809215.1	s__Heyndrickxia oleronia	76.7703	96	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.5507	103	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019645.1	s__Litchfieldia alkalitelluris	76.3203	64	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518865.1	s__Metabacillus sp000518865	76.2605	73	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107705.1	s__Neobacillus cucumis_B	76.1845	67	1566	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_002019635.1	s__Metabacillus halosaccharovorans	76.1454	76	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_902374955.1	s__Bacillus_AD massilioanorexius	76.141	53	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002844575.1	s__Margalitia camelliae	75.7823	97	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,820] [INFO] GTDB search result was written to GCF_017873565.1_ASM1787356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:01,821] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:01,825] [INFO] DFAST_QC result json was written to GCF_017873565.1_ASM1787356v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:01,825] [INFO] DFAST_QC completed!
[2024-01-24 13:42:01,825] [INFO] Total running time: 0h1m31s