[2024-01-24 12:14:48,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,775] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,775] [INFO] DQC Reference Directory: /var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference
[2024-01-24 12:14:50,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,091] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg63075911-81ac-442d-8028-842f87aacdbb/GCF_019711435.1_ASM1971143v1_genomic.fna.gz | prodigal -d GCF_019711435.1_ASM1971143v1_genomic.fna/cds.fna -a GCF_019711435.1_ASM1971143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:59,355] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:59,356] [INFO] Task started: HMMsearch
[2024-01-24 12:14:59,356] [INFO] Running command: hmmsearch --tblout GCF_019711435.1_ASM1971143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference/reference_markers.hmm GCF_019711435.1_ASM1971143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:59,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:59,614] [INFO] Found 6/6 markers.
[2024-01-24 12:14:59,644] [INFO] Query marker FASTA was written to GCF_019711435.1_ASM1971143v1_genomic.fna/markers.fasta
[2024-01-24 12:14:59,644] [INFO] Task started: Blastn
[2024-01-24 12:14:59,645] [INFO] Running command: blastn -query GCF_019711435.1_ASM1971143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference/reference_markers.fasta -out GCF_019711435.1_ASM1971143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,646] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,649] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:00,650] [INFO] Target genome list was writen to GCF_019711435.1_ASM1971143v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:00,652] [INFO] Task started: fastANI
[2024-01-24 12:15:00,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg63075911-81ac-442d-8028-842f87aacdbb/GCF_019711435.1_ASM1971143v1_genomic.fna.gz --refList GCF_019711435.1_ASM1971143v1_genomic.fna/target_genomes.txt --output GCF_019711435.1_ASM1971143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:07,436] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:07,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:07,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:07,446] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:07,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:07,446] [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
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	100.0	945	945	95	conclusive
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	85.3428	740	945	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	84.703	706	945	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	84.0618	683	945	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	83.9146	690	945	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	83.7485	662	945	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	83.2792	656	945	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.7583	625	945	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	81.6297	559	945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:07,448] [INFO] DFAST Taxonomy check result was written to GCF_019711435.1_ASM1971143v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:07,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:07,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:07,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference/checkm_data
[2024-01-24 12:15:07,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:07,484] [INFO] Task started: CheckM
[2024-01-24 12:15:07,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711435.1_ASM1971143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711435.1_ASM1971143v1_genomic.fna/checkm_input GCF_019711435.1_ASM1971143v1_genomic.fna/checkm_result
[2024-01-24 12:15:37,532] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:37,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,556] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:37,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:37,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711435.1_ASM1971143v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:37,557] [INFO] Task started: Blastn
[2024-01-24 12:15:37,558] [INFO] Running command: blastn -query GCF_019711435.1_ASM1971143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga686a8ed-edb1-4312-8c75-efafe9399f78/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711435.1_ASM1971143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:39,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:39,341] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:39,341] [INFO] Target genome list was writen to GCF_019711435.1_ASM1971143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:39,345] [INFO] Task started: fastANI
[2024-01-24 12:15:39,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg63075911-81ac-442d-8028-842f87aacdbb/GCF_019711435.1_ASM1971143v1_genomic.fna.gz --refList GCF_019711435.1_ASM1971143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711435.1_ASM1971143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:47,111] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:47,125] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:47,125] [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
GCA_000756795.1	s__Qipengyuania vulgaris_A	90.3976	797	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181515.1	s__Qipengyuania sp000181515	84.5731	691	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	83.0382	556	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	82.4447	635	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	82.0023	628	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	81.8365	602	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827325.1	s__Qipengyuania vulgaris	81.7378	611	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	81.5199	578	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	81.1794	437	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695185.1	s__Qipengyuania sp002695185	80.7638	481	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
GCF_009827295.1	s__Qipengyuania pelagi	80.0641	496	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	79.4039	395	945	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:47,128] [INFO] GTDB search result was written to GCF_019711435.1_ASM1971143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:47,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:47,133] [INFO] DFAST_QC result json was written to GCF_019711435.1_ASM1971143v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:47,133] [INFO] DFAST_QC completed!
[2024-01-24 12:15:47,133] [INFO] Total running time: 0h0m58s