[2024-01-24 14:55:24,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:24,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:24,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference
[2024-01-24 14:55:25,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:25,449] [INFO] Task started: Prodigal
[2024-01-24 14:55:25,450] [INFO] Running command: gunzip -c /var/lib/cwl/stgda77ae27-97e6-442b-9981-f433247fe1b2/GCF_019711535.1_ASM1971153v1_genomic.fna.gz | prodigal -d GCF_019711535.1_ASM1971153v1_genomic.fna/cds.fna -a GCF_019711535.1_ASM1971153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:34,548] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:34,549] [INFO] Task started: HMMsearch
[2024-01-24 14:55:34,549] [INFO] Running command: hmmsearch --tblout GCF_019711535.1_ASM1971153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference/reference_markers.hmm GCF_019711535.1_ASM1971153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:34,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:34,782] [INFO] Found 6/6 markers.
[2024-01-24 14:55:34,810] [INFO] Query marker FASTA was written to GCF_019711535.1_ASM1971153v1_genomic.fna/markers.fasta
[2024-01-24 14:55:34,811] [INFO] Task started: Blastn
[2024-01-24 14:55:34,811] [INFO] Running command: blastn -query GCF_019711535.1_ASM1971153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference/reference_markers.fasta -out GCF_019711535.1_ASM1971153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:35,665] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:35,668] [INFO] Selected 12 target genomes.
[2024-01-24 14:55:35,668] [INFO] Target genome list was writen to GCF_019711535.1_ASM1971153v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:35,692] [INFO] Task started: fastANI
[2024-01-24 14:55:35,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgda77ae27-97e6-442b-9981-f433247fe1b2/GCF_019711535.1_ASM1971153v1_genomic.fna.gz --refList GCF_019711535.1_ASM1971153v1_genomic.fna/target_genomes.txt --output GCF_019711535.1_ASM1971153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:43,302] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:43,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:43,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:43,313] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:43,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:43,314] [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 aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	100.0	975	975	95	conclusive
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	81.9597	555	975	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.7591	524	975	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	81.7431	549	975	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	81.4073	528	975	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	81.3382	535	975	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	81.3302	471	975	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	81.1889	516	975	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	81.1357	488	975	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	81.076	472	975	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.5127	455	975	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.5874	385	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:43,318] [INFO] DFAST Taxonomy check result was written to GCF_019711535.1_ASM1971153v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:43,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:43,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:43,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference/checkm_data
[2024-01-24 14:55:43,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:43,351] [INFO] Task started: CheckM
[2024-01-24 14:55:43,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711535.1_ASM1971153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711535.1_ASM1971153v1_genomic.fna/checkm_input GCF_019711535.1_ASM1971153v1_genomic.fna/checkm_result
[2024-01-24 14:56:13,564] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:13,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:13,583] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:13,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:13,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711535.1_ASM1971153v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:13,584] [INFO] Task started: Blastn
[2024-01-24 14:56:13,584] [INFO] Running command: blastn -query GCF_019711535.1_ASM1971153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78de4523-a34d-4f2d-abd9-c0c3e32fe59f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711535.1_ASM1971153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:15,081] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:15,084] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:15,084] [INFO] Target genome list was writen to GCF_019711535.1_ASM1971153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:15,100] [INFO] Task started: fastANI
[2024-01-24 14:56:15,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgda77ae27-97e6-442b-9981-f433247fe1b2/GCF_019711535.1_ASM1971153v1_genomic.fna.gz --refList GCF_019711535.1_ASM1971153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711535.1_ASM1971153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:23,347] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:23,359] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:56:23,360] [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_002695185.1	s__Qipengyuania sp002695185	84.7258	632	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
GCF_000181515.1	s__Qipengyuania sp000181515	81.6634	531	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	81.439	524	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911865.1	s__Qipengyuania sp013911865	80.925	400	975	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	80.8281	500	975	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	80.7243	422	975	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	80.6857	492	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	80.6252	474	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_001542855.1	s__Qipengyuania sp001542855	80.5901	483	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009827445.1	s__Qipengyuania aquimaris	80.3162	461	975	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	80.2911	343	975	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	80.1615	477	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.5874	385	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	79.0594	359	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,363] [INFO] GTDB search result was written to GCF_019711535.1_ASM1971153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:23,364] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:23,368] [INFO] DFAST_QC result json was written to GCF_019711535.1_ASM1971153v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:23,368] [INFO] DFAST_QC completed!
[2024-01-24 14:56:23,368] [INFO] Total running time: 0h0m59s