[2024-01-24 12:46:57,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference
[2024-01-24 12:46:59,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:59,258] [INFO] Task started: Prodigal
[2024-01-24 12:46:59,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f81bcd2-34a0-4e07-bec6-636894d4593c/GCF_011762005.1_ASM1176200v1_genomic.fna.gz | prodigal -d GCF_011762005.1_ASM1176200v1_genomic.fna/cds.fna -a GCF_011762005.1_ASM1176200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:07,872] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:07,873] [INFO] Task started: HMMsearch
[2024-01-24 12:47:07,873] [INFO] Running command: hmmsearch --tblout GCF_011762005.1_ASM1176200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference/reference_markers.hmm GCF_011762005.1_ASM1176200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:08,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:08,109] [INFO] Found 6/6 markers.
[2024-01-24 12:47:08,147] [INFO] Query marker FASTA was written to GCF_011762005.1_ASM1176200v1_genomic.fna/markers.fasta
[2024-01-24 12:47:08,148] [INFO] Task started: Blastn
[2024-01-24 12:47:08,148] [INFO] Running command: blastn -query GCF_011762005.1_ASM1176200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference/reference_markers.fasta -out GCF_011762005.1_ASM1176200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:09,038] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:09,041] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:09,042] [INFO] Target genome list was writen to GCF_011762005.1_ASM1176200v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:09,046] [INFO] Task started: fastANI
[2024-01-24 12:47:09,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f81bcd2-34a0-4e07-bec6-636894d4593c/GCF_011762005.1_ASM1176200v1_genomic.fna.gz --refList GCF_011762005.1_ASM1176200v1_genomic.fna/target_genomes.txt --output GCF_011762005.1_ASM1176200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:17,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:17,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:17,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:17,752] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:17,753] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:17,753] [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 flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	100.0	935	935	95	conclusive
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.7393	604	935	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.6294	614	935	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.0266	537	935	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.9709	574	935	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.9194	546	935	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	80.8665	534	935	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.8148	542	935	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	80.6186	549	935	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	80.5975	557	935	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	80.5305	566	935	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	80.4633	499	935	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	80.2103	511	935	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	80.208	448	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:17,754] [INFO] DFAST Taxonomy check result was written to GCF_011762005.1_ASM1176200v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:17,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:17,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:17,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference/checkm_data
[2024-01-24 12:47:17,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:17,785] [INFO] Task started: CheckM
[2024-01-24 12:47:17,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011762005.1_ASM1176200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011762005.1_ASM1176200v1_genomic.fna/checkm_input GCF_011762005.1_ASM1176200v1_genomic.fna/checkm_result
[2024-01-24 12:47:47,958] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:47,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:47,976] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:47,976] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:47,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011762005.1_ASM1176200v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:47,977] [INFO] Task started: Blastn
[2024-01-24 12:47:47,977] [INFO] Running command: blastn -query GCF_011762005.1_ASM1176200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7fda050-d8db-46f4-aacd-7460f9a4c634/dqc_reference/reference_markers_gtdb.fasta -out GCF_011762005.1_ASM1176200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:49,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:49,746] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:49,746] [INFO] Target genome list was writen to GCF_011762005.1_ASM1176200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:49,751] [INFO] Task started: fastANI
[2024-01-24 12:47:49,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f81bcd2-34a0-4e07-bec6-636894d4593c/GCF_011762005.1_ASM1176200v1_genomic.fna.gz --refList GCF_011762005.1_ASM1176200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011762005.1_ASM1176200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:57,841] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:57,858] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:57,858] [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_011762005.1	s__Qipengyuania flava	100.0	935	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	conclusive
GCF_009828015.1	s__Qipengyuania citrea	84.906	737	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_016764075.1	s__Qipengyuania sp016764075	84.5041	532	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	82.6566	676	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_003355455.1	s__Qipengyuania aurea	82.1616	637	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_009827315.1	s__Qipengyuania gaetbuli	80.9636	574	935	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	80.6298	548	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	80.5886	561	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCA_013001165.1	s__Qipengyuania sp013001165	80.2334	436	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	80.0314	424	935	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	79.983	468	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	79.868	524	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:57,860] [INFO] GTDB search result was written to GCF_011762005.1_ASM1176200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:57,860] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:57,863] [INFO] DFAST_QC result json was written to GCF_011762005.1_ASM1176200v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:57,863] [INFO] DFAST_QC completed!
[2024-01-24 12:47:57,864] [INFO] Total running time: 0h1m0s