[2024-01-24 14:30:17,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:17,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:17,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference
[2024-01-24 14:30:18,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,592] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg07d8b24a-96c9-446b-8706-7d7f17cf6839/GCF_019711635.1_ASM1971163v1_genomic.fna.gz | prodigal -d GCF_019711635.1_ASM1971163v1_genomic.fna/cds.fna -a GCF_019711635.1_ASM1971163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:26,293] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:26,293] [INFO] Task started: HMMsearch
[2024-01-24 14:30:26,293] [INFO] Running command: hmmsearch --tblout GCF_019711635.1_ASM1971163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference/reference_markers.hmm GCF_019711635.1_ASM1971163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:26,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:26,537] [INFO] Found 6/6 markers.
[2024-01-24 14:30:26,566] [INFO] Query marker FASTA was written to GCF_019711635.1_ASM1971163v1_genomic.fna/markers.fasta
[2024-01-24 14:30:26,567] [INFO] Task started: Blastn
[2024-01-24 14:30:26,567] [INFO] Running command: blastn -query GCF_019711635.1_ASM1971163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference/reference_markers.fasta -out GCF_019711635.1_ASM1971163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:27,372] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:27,376] [INFO] Selected 17 target genomes.
[2024-01-24 14:30:27,377] [INFO] Target genome list was writen to GCF_019711635.1_ASM1971163v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:27,503] [INFO] Task started: fastANI
[2024-01-24 14:30:27,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg07d8b24a-96c9-446b-8706-7d7f17cf6839/GCF_019711635.1_ASM1971163v1_genomic.fna.gz --refList GCF_019711635.1_ASM1971163v1_genomic.fna/target_genomes.txt --output GCF_019711635.1_ASM1971163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:38,273] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:38,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:38,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:38,288] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:38,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:38,289] [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 huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	100.0	837	838	95	conclusive
Qipengyuania vulgaris	strain=DSM 17792	GCA_009827325.1	291985	291985	type	True	87.9543	686	838	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	82.2283	581	838	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	82.0016	551	838	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	81.8827	554	838	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	81.7502	555	838	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	81.7487	545	838	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	81.7187	556	838	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	81.3202	534	838	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	81.0231	531	838	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	81.0081	480	838	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.7803	491	838	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	80.7507	493	838	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.4979	397	838	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	79.4421	410	838	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.9977	263	838	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.9908	216	838	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:38,290] [INFO] DFAST Taxonomy check result was written to GCF_019711635.1_ASM1971163v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:38,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:38,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:38,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference/checkm_data
[2024-01-24 14:30:38,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:38,325] [INFO] Task started: CheckM
[2024-01-24 14:30:38,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711635.1_ASM1971163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711635.1_ASM1971163v1_genomic.fna/checkm_input GCF_019711635.1_ASM1971163v1_genomic.fna/checkm_result
[2024-01-24 14:31:07,015] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:07,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:07,035] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:07,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:07,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711635.1_ASM1971163v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:07,036] [INFO] Task started: Blastn
[2024-01-24 14:31:07,036] [INFO] Running command: blastn -query GCF_019711635.1_ASM1971163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c9ebcc-eeef-45f1-9a80-0a09888150b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711635.1_ASM1971163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:08,275] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:08,280] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:08,280] [INFO] Target genome list was writen to GCF_019711635.1_ASM1971163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:08,297] [INFO] Task started: fastANI
[2024-01-24 14:31:08,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg07d8b24a-96c9-446b-8706-7d7f17cf6839/GCF_019711635.1_ASM1971163v1_genomic.fna.gz --refList GCF_019711635.1_ASM1971163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711635.1_ASM1971163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:16,749] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:16,761] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:16,761] [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_013911865.1	s__Qipengyuania sp013911865	98.1302	641	838	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827325.1	s__Qipengyuania vulgaris	87.9543	686	838	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	81.8195	576	838	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	81.7675	560	838	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	81.1262	452	838	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	81.0231	531	838	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	80.7501	493	838	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	80.6243	413	838	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
GCA_016764075.1	s__Qipengyuania sp016764075	80.572	369	838	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	80.484	464	838	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	80.3368	442	838	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.0365	264	838	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827305.1	s__Croceibacterium xixiisoli	77.9908	216	838	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:16,763] [INFO] GTDB search result was written to GCF_019711635.1_ASM1971163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:16,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:16,769] [INFO] DFAST_QC result json was written to GCF_019711635.1_ASM1971163v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:16,769] [INFO] DFAST_QC completed!
[2024-01-24 14:31:16,769] [INFO] Total running time: 0h0m60s