[2024-01-24 13:17:13,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,865] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,865] [INFO] DQC Reference Directory: /var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference
[2024-01-24 13:17:15,272] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,273] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,273] [INFO] Running command: gunzip -c /var/lib/cwl/stg71f38775-7e09-4987-81cc-ed6d1b96f373/GCF_019857185.1_ASM1985718v1_genomic.fna.gz | prodigal -d GCF_019857185.1_ASM1985718v1_genomic.fna/cds.fna -a GCF_019857185.1_ASM1985718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:24,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:24,428] [INFO] Task started: HMMsearch
[2024-01-24 13:17:24,428] [INFO] Running command: hmmsearch --tblout GCF_019857185.1_ASM1985718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference/reference_markers.hmm GCF_019857185.1_ASM1985718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:24,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:24,704] [INFO] Found 6/6 markers.
[2024-01-24 13:17:24,742] [INFO] Query marker FASTA was written to GCF_019857185.1_ASM1985718v1_genomic.fna/markers.fasta
[2024-01-24 13:17:24,742] [INFO] Task started: Blastn
[2024-01-24 13:17:24,743] [INFO] Running command: blastn -query GCF_019857185.1_ASM1985718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference/reference_markers.fasta -out GCF_019857185.1_ASM1985718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:25,723] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:25,728] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:25,729] [INFO] Target genome list was writen to GCF_019857185.1_ASM1985718v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:25,736] [INFO] Task started: fastANI
[2024-01-24 13:17:25,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f38775-7e09-4987-81cc-ed6d1b96f373/GCF_019857185.1_ASM1985718v1_genomic.fna.gz --refList GCF_019857185.1_ASM1985718v1_genomic.fna/target_genomes.txt --output GCF_019857185.1_ASM1985718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:35,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:35,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:35,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:35,675] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:35,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:35,676] [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
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	100.0	1027	1028	95	conclusive
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	85.3113	750	1028	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	85.2634	765	1028	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	80.1954	503	1028	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.1491	490	1028	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.0253	509	1028	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.7916	489	1028	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.7716	424	1028	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.6225	440	1028	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.5854	470	1028	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.4143	474	1028	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.3535	440	1028	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.1331	412	1028	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.0854	413	1028	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.8179	358	1028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:35,677] [INFO] DFAST Taxonomy check result was written to GCF_019857185.1_ASM1985718v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:35,678] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:35,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:35,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference/checkm_data
[2024-01-24 13:17:35,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:35,711] [INFO] Task started: CheckM
[2024-01-24 13:17:35,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019857185.1_ASM1985718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019857185.1_ASM1985718v1_genomic.fna/checkm_input GCF_019857185.1_ASM1985718v1_genomic.fna/checkm_result
[2024-01-24 13:18:06,881] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:06,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:06,906] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:06,906] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:06,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019857185.1_ASM1985718v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:06,907] [INFO] Task started: Blastn
[2024-01-24 13:18:06,907] [INFO] Running command: blastn -query GCF_019857185.1_ASM1985718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0438947f-3dfe-45e4-95c9-cd292f5f2a08/dqc_reference/reference_markers_gtdb.fasta -out GCF_019857185.1_ASM1985718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,722] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,726] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:08,727] [INFO] Target genome list was writen to GCF_019857185.1_ASM1985718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:08,734] [INFO] Task started: fastANI
[2024-01-24 13:18:08,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f38775-7e09-4987-81cc-ed6d1b96f373/GCF_019857185.1_ASM1985718v1_genomic.fna.gz --refList GCF_019857185.1_ASM1985718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019857185.1_ASM1985718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:14,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:14,880] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:14,880] [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_000176355.1	s__Alteriqipengyuania bathyomarina	94.636	926	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	94.3787	906	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	85.6501	705	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	85.2634	765	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	84.9515	761	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	84.7037	747	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	84.524	728	1028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	84.4551	396	1028	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 13:18:14,882] [INFO] GTDB search result was written to GCF_019857185.1_ASM1985718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:14,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:14,886] [INFO] DFAST_QC result json was written to GCF_019857185.1_ASM1985718v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:14,886] [INFO] DFAST_QC completed!
[2024-01-24 13:18:14,886] [INFO] Total running time: 0h1m1s