[2024-01-25 18:00:20,740] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference
[2024-01-25 18:00:21,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:21,882] [INFO] Task started: Prodigal
[2024-01-25 18:00:21,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg32a11af2-d94e-4124-ada9-c7c5e0ff9416/GCF_000265385.1_ASM26538v1_genomic.fna.gz | prodigal -d GCF_000265385.1_ASM26538v1_genomic.fna/cds.fna -a GCF_000265385.1_ASM26538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:33,743] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:33,743] [INFO] Task started: HMMsearch
[2024-01-25 18:00:33,743] [INFO] Running command: hmmsearch --tblout GCF_000265385.1_ASM26538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference/reference_markers.hmm GCF_000265385.1_ASM26538v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:34,004] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:34,005] [INFO] Found 6/6 markers.
[2024-01-25 18:00:34,032] [INFO] Query marker FASTA was written to GCF_000265385.1_ASM26538v1_genomic.fna/markers.fasta
[2024-01-25 18:00:34,032] [INFO] Task started: Blastn
[2024-01-25 18:00:34,032] [INFO] Running command: blastn -query GCF_000265385.1_ASM26538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference/reference_markers.fasta -out GCF_000265385.1_ASM26538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:34,654] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:34,657] [INFO] Selected 13 target genomes.
[2024-01-25 18:00:34,657] [INFO] Target genome list was writen to GCF_000265385.1_ASM26538v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:34,675] [INFO] Task started: fastANI
[2024-01-25 18:00:34,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg32a11af2-d94e-4124-ada9-c7c5e0ff9416/GCF_000265385.1_ASM26538v1_genomic.fna.gz --refList GCF_000265385.1_ASM26538v1_genomic.fna/target_genomes.txt --output GCF_000265385.1_ASM26538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:43,806] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:43,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:43,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:43,814] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:00:43,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:43,815] [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
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	100.0	1173	1173	95	conclusive
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	80.7249	740	1173	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	80.6301	667	1173	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.4679	669	1173	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	79.556	573	1173	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	79.5109	589	1173	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	79.508	551	1173	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	79.2451	605	1173	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.4442	56	1173	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.4311	62	1173	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.2896	80	1173	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2876	70	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:43,818] [INFO] DFAST Taxonomy check result was written to GCF_000265385.1_ASM26538v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:43,818] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:43,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:43,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference/checkm_data
[2024-01-25 18:00:43,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:43,854] [INFO] Task started: CheckM
[2024-01-25 18:00:43,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000265385.1_ASM26538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000265385.1_ASM26538v1_genomic.fna/checkm_input GCF_000265385.1_ASM26538v1_genomic.fna/checkm_result
[2024-01-25 18:01:20,544] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:20,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:20,572] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:20,572] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:20,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000265385.1_ASM26538v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:20,573] [INFO] Task started: Blastn
[2024-01-25 18:01:20,573] [INFO] Running command: blastn -query GCF_000265385.1_ASM26538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecb6f1ed-6258-4091-a0d3-3f5a80bd967d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000265385.1_ASM26538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:21,511] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:21,514] [INFO] Selected 11 target genomes.
[2024-01-25 18:01:21,514] [INFO] Target genome list was writen to GCF_000265385.1_ASM26538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:21,531] [INFO] Task started: fastANI
[2024-01-25 18:01:21,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg32a11af2-d94e-4124-ada9-c7c5e0ff9416/GCF_000265385.1_ASM26538v1_genomic.fna.gz --refList GCF_000265385.1_ASM26538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000265385.1_ASM26538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:30,288] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:30,296] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:30,296] [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_000265385.1	s__Aequorivita sublithincola	100.0	1173	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007997155.1	s__Aequorivita antarctica	80.7502	737	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900489465.1	s__Aequorivita sp900489465	80.727	679	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	80.7165	643	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	80.6335	666	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_007997135.1	s__Aequorivita lipolytica	80.4646	669	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002364215.1	s__Aequorivita sp002364215	79.7502	593	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001573155.1	s__Aequorivita aquimaris	79.556	573	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	79.5315	589	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	79.508	551	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_000429125.1	s__Aequorivita capsosiphonis	79.2451	605	1173	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:30,298] [INFO] GTDB search result was written to GCF_000265385.1_ASM26538v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:30,299] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:30,302] [INFO] DFAST_QC result json was written to GCF_000265385.1_ASM26538v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:30,302] [INFO] DFAST_QC completed!
[2024-01-25 18:01:30,302] [INFO] Total running time: 0h1m10s