[2024-01-24 13:21:47,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference
[2024-01-24 13:21:48,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,600] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg38528c71-4938-4ed0-b180-608185478c22/GCF_001461885.1_ASM146188v1_genomic.fna.gz | prodigal -d GCF_001461885.1_ASM146188v1_genomic.fna/cds.fna -a GCF_001461885.1_ASM146188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:57,267] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:57,268] [INFO] Task started: HMMsearch
[2024-01-24 13:21:57,268] [INFO] Running command: hmmsearch --tblout GCF_001461885.1_ASM146188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference/reference_markers.hmm GCF_001461885.1_ASM146188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:57,523] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:57,525] [INFO] Found 6/6 markers.
[2024-01-24 13:21:57,555] [INFO] Query marker FASTA was written to GCF_001461885.1_ASM146188v1_genomic.fna/markers.fasta
[2024-01-24 13:21:57,555] [INFO] Task started: Blastn
[2024-01-24 13:21:57,555] [INFO] Running command: blastn -query GCF_001461885.1_ASM146188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference/reference_markers.fasta -out GCF_001461885.1_ASM146188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:58,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:58,477] [INFO] Selected 12 target genomes.
[2024-01-24 13:21:58,478] [INFO] Target genome list was writen to GCF_001461885.1_ASM146188v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:58,484] [INFO] Task started: fastANI
[2024-01-24 13:21:58,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg38528c71-4938-4ed0-b180-608185478c22/GCF_001461885.1_ASM146188v1_genomic.fna.gz --refList GCF_001461885.1_ASM146188v1_genomic.fna/target_genomes.txt --output GCF_001461885.1_ASM146188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:06,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:06,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:06,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:06,248] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:06,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:06,249] [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 marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	100.0	960	961	95	conclusive
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	99.9966	957	961	95	conclusive
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	85.7811	736	961	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	81.4574	615	961	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	81.2919	633	961	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.3612	432	961	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.3017	415	961	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.2754	421	961	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.0057	365	961	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.9116	414	961	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.8089	365	961	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.6881	396	961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:06,252] [INFO] DFAST Taxonomy check result was written to GCF_001461885.1_ASM146188v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:06,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:06,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:06,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference/checkm_data
[2024-01-24 13:22:06,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:06,291] [INFO] Task started: CheckM
[2024-01-24 13:22:06,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001461885.1_ASM146188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001461885.1_ASM146188v1_genomic.fna/checkm_input GCF_001461885.1_ASM146188v1_genomic.fna/checkm_result
[2024-01-24 13:22:36,152] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:36,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,172] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:36,173] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:36,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001461885.1_ASM146188v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:36,174] [INFO] Task started: Blastn
[2024-01-24 13:22:36,174] [INFO] Running command: blastn -query GCF_001461885.1_ASM146188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd18335d2-1abc-4b6e-934b-6159cd97d0e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001461885.1_ASM146188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:37,893] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:37,896] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:37,896] [INFO] Target genome list was writen to GCF_001461885.1_ASM146188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:38,845] [INFO] Task started: fastANI
[2024-01-24 13:22:38,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg38528c71-4938-4ed0-b180-608185478c22/GCF_001461885.1_ASM146188v1_genomic.fna.gz --refList GCF_001461885.1_ASM146188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001461885.1_ASM146188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:47,712] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:47,725] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:47,725] [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_001028625.1	s__Pelagerythrobacter marensis	99.9966	957	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009827515.1	s__Pelagerythrobacter marinus	85.7811	736	961	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	81.4364	617	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	81.3877	633	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	81.2987	633	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	79.3635	417	961	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	79.2774	420	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	79.2442	394	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.9861	418	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	78.9224	413	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007065885.1	s__Tsuneonella sp007065885	78.8594	378	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644315.1	s__Tsuneonella deserti	78.6973	334	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005884405.1	s__Qipengyuania marisflavi	78.6794	344	961	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 13:22:47,727] [INFO] GTDB search result was written to GCF_001461885.1_ASM146188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:47,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:47,731] [INFO] DFAST_QC result json was written to GCF_001461885.1_ASM146188v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:47,731] [INFO] DFAST_QC completed!
[2024-01-24 13:22:47,731] [INFO] Total running time: 0h1m0s