[2024-01-24 14:05:00,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,829] [INFO] DQC Reference Directory: /var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference
[2024-01-24 14:05:01,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,972] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b0eef7f-c3a8-4ecd-a629-5b62362f6c29/GCF_016890225.1_ASM1689022v1_genomic.fna.gz | prodigal -d GCF_016890225.1_ASM1689022v1_genomic.fna/cds.fna -a GCF_016890225.1_ASM1689022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:09,244] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:09,245] [INFO] Task started: HMMsearch
[2024-01-24 14:05:09,245] [INFO] Running command: hmmsearch --tblout GCF_016890225.1_ASM1689022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference/reference_markers.hmm GCF_016890225.1_ASM1689022v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:09,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:09,458] [INFO] Found 6/6 markers.
[2024-01-24 14:05:09,491] [INFO] Query marker FASTA was written to GCF_016890225.1_ASM1689022v1_genomic.fna/markers.fasta
[2024-01-24 14:05:09,491] [INFO] Task started: Blastn
[2024-01-24 14:05:09,491] [INFO] Running command: blastn -query GCF_016890225.1_ASM1689022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference/reference_markers.fasta -out GCF_016890225.1_ASM1689022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:10,052] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:10,055] [INFO] Selected 22 target genomes.
[2024-01-24 14:05:10,055] [INFO] Target genome list was writen to GCF_016890225.1_ASM1689022v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:10,153] [INFO] Task started: fastANI
[2024-01-24 14:05:10,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b0eef7f-c3a8-4ecd-a629-5b62362f6c29/GCF_016890225.1_ASM1689022v1_genomic.fna.gz --refList GCF_016890225.1_ASM1689022v1_genomic.fna/target_genomes.txt --output GCF_016890225.1_ASM1689022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:24,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:24,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:24,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:24,777] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:24,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:24,778] [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
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	100.0	1278	1283	95	conclusive
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	78.0681	248	1283	95	below_threshold
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	78.0678	244	1283	95	below_threshold
Niallia taxi	strain=M5HDSG1-1	GCA_004005475.1	2499688	2499688	type	True	77.2311	59	1283	95	below_threshold
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	77.216	91	1283	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.1676	118	1283	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	77.1529	147	1283	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	77.0571	98	1283	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	77.056	148	1283	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	77.0546	99	1283	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	77.0486	82	1283	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	77.0283	55	1283	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.9194	106	1283	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	76.9102	88	1283	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.9046	94	1283	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.7984	91	1283	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.7734	113	1283	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.7705	110	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:24,780] [INFO] DFAST Taxonomy check result was written to GCF_016890225.1_ASM1689022v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:24,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:24,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:24,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference/checkm_data
[2024-01-24 14:05:24,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:24,821] [INFO] Task started: CheckM
[2024-01-24 14:05:24,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016890225.1_ASM1689022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016890225.1_ASM1689022v1_genomic.fna/checkm_input GCF_016890225.1_ASM1689022v1_genomic.fna/checkm_result
[2024-01-24 14:05:53,659] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:53,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:53,686] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:53,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:53,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016890225.1_ASM1689022v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:53,687] [INFO] Task started: Blastn
[2024-01-24 14:05:53,687] [INFO] Running command: blastn -query GCF_016890225.1_ASM1689022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc662c248-c4a9-4fab-a2a5-3331051ee9af/dqc_reference/reference_markers_gtdb.fasta -out GCF_016890225.1_ASM1689022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:54,649] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:54,654] [INFO] Selected 22 target genomes.
[2024-01-24 14:05:54,654] [INFO] Target genome list was writen to GCF_016890225.1_ASM1689022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:54,671] [INFO] Task started: fastANI
[2024-01-24 14:05:54,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b0eef7f-c3a8-4ecd-a629-5b62362f6c29/GCF_016890225.1_ASM1689022v1_genomic.fna.gz --refList GCF_016890225.1_ASM1689022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016890225.1_ASM1689022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:11,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:11,419] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:11,420] [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_016890225.1	s__Bacillus_BS sp016890225	100.0	1278	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008364785.1	s__Bacillus_BS sp008364785	83.601	948	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008845.1	s__Bacillus_BS mesophilus	78.0466	246	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	77.1944	95	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873715.1	s__Bacillus_BV luteolus	77.1887	145	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014837155.1	s__Litchfieldia sp014837155	77.173	129	1283	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_016909075.1	s__Priestia iocasae	77.1452	98	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	77.1106	130	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591585.1	s__Niallia circulans	77.0486	82	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
GCF_900156865.1	s__Fredinandcohnia sinesaloumensis	77.0287	95	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	76.9772	133	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_001648555.1	s__Rossellomorea aquimaris	76.883	89	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002560985.1	s__Bacillus_A sp002560985	76.8661	101	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157855.1	s__Sutcliffiella_A horikoshii_C	76.8355	97	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	96.53	95.82	0.92	0.90	4	-
GCF_008180335.1	s__Priestia megaterium_B	76.8268	92	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019219025.1	s__Neobacillus sp019219025	76.8187	96	1283	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_002156865.1	s__Gottfriedia luciferensis	76.7984	91	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	76.7877	111	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917645.1	s__Robertmurraya sp009917645	76.7779	94	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757995.1	s__Bacillus_A mycoides_B	76.6995	116	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.94	99.86	0.98	0.98	4	-
GCF_001591485.1	s__Neobacillus fumarioli	76.3837	53	1283	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_011524525.1	s__Robertmurraya sp011524525	76.0774	69	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:11,421] [INFO] GTDB search result was written to GCF_016890225.1_ASM1689022v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:11,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:11,426] [INFO] DFAST_QC result json was written to GCF_016890225.1_ASM1689022v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:11,426] [INFO] DFAST_QC completed!
[2024-01-24 14:06:11,426] [INFO] Total running time: 0h1m11s