[2024-01-24 12:40:08,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference
[2024-01-24 12:40:09,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,595] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgf661f8d9-6372-4f78-8e1e-4d0f7d4cd6ce/GCF_003581645.1_ASM358164v1_genomic.fna.gz | prodigal -d GCF_003581645.1_ASM358164v1_genomic.fna/cds.fna -a GCF_003581645.1_ASM358164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:20,247] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:20,248] [INFO] Task started: HMMsearch
[2024-01-24 12:40:20,248] [INFO] Running command: hmmsearch --tblout GCF_003581645.1_ASM358164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference/reference_markers.hmm GCF_003581645.1_ASM358164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:20,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:20,515] [INFO] Found 6/6 markers.
[2024-01-24 12:40:20,553] [INFO] Query marker FASTA was written to GCF_003581645.1_ASM358164v1_genomic.fna/markers.fasta
[2024-01-24 12:40:20,553] [INFO] Task started: Blastn
[2024-01-24 12:40:20,553] [INFO] Running command: blastn -query GCF_003581645.1_ASM358164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference/reference_markers.fasta -out GCF_003581645.1_ASM358164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:21,614] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:21,617] [INFO] Selected 11 target genomes.
[2024-01-24 12:40:21,618] [INFO] Target genome list was writen to GCF_003581645.1_ASM358164v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:21,622] [INFO] Task started: fastANI
[2024-01-24 12:40:21,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgf661f8d9-6372-4f78-8e1e-4d0f7d4cd6ce/GCF_003581645.1_ASM358164v1_genomic.fna.gz --refList GCF_003581645.1_ASM358164v1_genomic.fna/target_genomes.txt --output GCF_003581645.1_ASM358164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:29,327] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:29,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:29,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:29,339] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:29,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:29,339] [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
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	100.0	1180	1210	95	conclusive
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	88.8605	818	1210	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	83.2433	693	1210	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	81.2453	632	1210	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	81.2107	643	1210	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.0489	509	1210	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.9658	495	1210	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	79.5924	465	1210	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.2769	446	1210	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.0393	412	1210	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.0074	369	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:29,341] [INFO] DFAST Taxonomy check result was written to GCF_003581645.1_ASM358164v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:29,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:29,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:29,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference/checkm_data
[2024-01-24 12:40:29,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:29,385] [INFO] Task started: CheckM
[2024-01-24 12:40:29,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003581645.1_ASM358164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003581645.1_ASM358164v1_genomic.fna/checkm_input GCF_003581645.1_ASM358164v1_genomic.fna/checkm_result
[2024-01-24 12:41:02,925] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:02,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:02,950] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:02,951] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:02,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003581645.1_ASM358164v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:02,952] [INFO] Task started: Blastn
[2024-01-24 12:41:02,952] [INFO] Running command: blastn -query GCF_003581645.1_ASM358164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3acd8923-750d-4b7a-b8b1-e84f2720dcee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003581645.1_ASM358164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:04,869] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:04,873] [INFO] Selected 9 target genomes.
[2024-01-24 12:41:04,873] [INFO] Target genome list was writen to GCF_003581645.1_ASM358164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:04,881] [INFO] Task started: fastANI
[2024-01-24 12:41:04,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgf661f8d9-6372-4f78-8e1e-4d0f7d4cd6ce/GCF_003581645.1_ASM358164v1_genomic.fna.gz --refList GCF_003581645.1_ASM358164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003581645.1_ASM358164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:11,335] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:11,343] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:11,343] [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_003581645.1	s__Pelagerythrobacter aerophilus	100.0	1175	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016803135.1	s__Pelagerythrobacter sp016803135	89.6644	873	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	88.885	817	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	83.2312	694	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	81.2428	633	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001542855.1	s__Qipengyuania sp001542855	80.4344	504	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009828015.1	s__Qipengyuania citrea	79.8257	467	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	79.6371	471	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.5829	463	1210	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 12:41:11,345] [INFO] GTDB search result was written to GCF_003581645.1_ASM358164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:11,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:11,351] [INFO] DFAST_QC result json was written to GCF_003581645.1_ASM358164v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:11,352] [INFO] DFAST_QC completed!
[2024-01-24 12:41:11,352] [INFO] Total running time: 0h1m3s