[2024-01-24 12:46:57,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference
[2024-01-24 12:46:59,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:59,395] [INFO] Task started: Prodigal
[2024-01-24 12:46:59,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg27e40c14-c156-4694-b67f-60611af7c11a/GCF_011742875.1_ASM1174287v1_genomic.fna.gz | prodigal -d GCF_011742875.1_ASM1174287v1_genomic.fna/cds.fna -a GCF_011742875.1_ASM1174287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:13,022] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:13,022] [INFO] Task started: HMMsearch
[2024-01-24 12:47:13,023] [INFO] Running command: hmmsearch --tblout GCF_011742875.1_ASM1174287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference/reference_markers.hmm GCF_011742875.1_ASM1174287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:13,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:13,318] [INFO] Found 6/6 markers.
[2024-01-24 12:47:13,358] [INFO] Query marker FASTA was written to GCF_011742875.1_ASM1174287v1_genomic.fna/markers.fasta
[2024-01-24 12:47:13,359] [INFO] Task started: Blastn
[2024-01-24 12:47:13,359] [INFO] Running command: blastn -query GCF_011742875.1_ASM1174287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference/reference_markers.fasta -out GCF_011742875.1_ASM1174287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:14,290] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:14,293] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:14,293] [INFO] Target genome list was writen to GCF_011742875.1_ASM1174287v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:14,300] [INFO] Task started: fastANI
[2024-01-24 12:47:14,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg27e40c14-c156-4694-b67f-60611af7c11a/GCF_011742875.1_ASM1174287v1_genomic.fna.gz --refList GCF_011742875.1_ASM1174287v1_genomic.fna/target_genomes.txt --output GCF_011742875.1_ASM1174287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:30,337] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:30,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:30,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:30,352] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:30,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:30,352] [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
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	100.0	1405	1405	95	conclusive
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	85.1878	1039	1405	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	82.5811	829	1405	95	below_threshold
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	82.4505	910	1405	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	82.4146	892	1405	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	82.2863	784	1405	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.7488	523	1405	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.7311	576	1405	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.6864	558	1405	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.4619	448	1405	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.9235	514	1405	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.3446	362	1405	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.6355	120	1405	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.5887	120	1405	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.5242	83	1405	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.2987	131	1405	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.8997	75	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,355] [INFO] DFAST Taxonomy check result was written to GCF_011742875.1_ASM1174287v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:30,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:30,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:30,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference/checkm_data
[2024-01-24 12:47:30,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:30,402] [INFO] Task started: CheckM
[2024-01-24 12:47:30,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011742875.1_ASM1174287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011742875.1_ASM1174287v1_genomic.fna/checkm_input GCF_011742875.1_ASM1174287v1_genomic.fna/checkm_result
[2024-01-24 12:48:14,719] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:14,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:14,738] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:14,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:14,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011742875.1_ASM1174287v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:14,740] [INFO] Task started: Blastn
[2024-01-24 12:48:14,740] [INFO] Running command: blastn -query GCF_011742875.1_ASM1174287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46ad476f-64ed-4df1-9b4c-7a99b2531769/dqc_reference/reference_markers_gtdb.fasta -out GCF_011742875.1_ASM1174287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:16,291] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:16,294] [INFO] Selected 14 target genomes.
[2024-01-24 12:48:16,294] [INFO] Target genome list was writen to GCF_011742875.1_ASM1174287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:16,305] [INFO] Task started: fastANI
[2024-01-24 12:48:16,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg27e40c14-c156-4694-b67f-60611af7c11a/GCF_011742875.1_ASM1174287v1_genomic.fna.gz --refList GCF_011742875.1_ASM1174287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011742875.1_ASM1174287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:29,001] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:29,022] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:29,022] [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_011742875.1	s__Luteibacter yeojuensis	100.0	1405	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011742555.1	s__Luteibacter jiangsuensis	85.2076	1036	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759605.1	s__Luteibacter sp011759605	85.1407	1030	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110505.1	s__Luteibacter sp900110505	84.2672	931	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	97.58	97.58	0.93	0.93	2	-
GCF_900109915.1	s__Luteibacter sp900109915	83.8241	916	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119235.1	s__Luteibacter sp900119235	83.5776	900	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912395.1	s__Luteibacter sp009912395	83.0222	878	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745005.1	s__Luteibacter sp000745005	82.6701	851	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018889975.1	s__Luteibacter sp018889975	82.6213	892	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759365.1	s__Luteibacter anthropi	82.5549	832	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868105.1	s__RBG-16-66-20 sp016868105	76.3348	104	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__RBG-16-66-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898725.1	s__UBA4615 sp903898725	75.5741	155	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:29,024] [INFO] GTDB search result was written to GCF_011742875.1_ASM1174287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:29,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:29,028] [INFO] DFAST_QC result json was written to GCF_011742875.1_ASM1174287v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:29,028] [INFO] DFAST_QC completed!
[2024-01-24 12:48:29,029] [INFO] Total running time: 0h1m31s