[2024-01-24 11:13:04,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference
[2024-01-24 11:13:05,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,790] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ac175fe-c43c-4ddf-bee1-3750e735d41f/GCF_016907015.1_ASM1690701v1_genomic.fna.gz | prodigal -d GCF_016907015.1_ASM1690701v1_genomic.fna/cds.fna -a GCF_016907015.1_ASM1690701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:15,509] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:15,509] [INFO] Task started: HMMsearch
[2024-01-24 11:13:15,509] [INFO] Running command: hmmsearch --tblout GCF_016907015.1_ASM1690701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference/reference_markers.hmm GCF_016907015.1_ASM1690701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:15,807] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:15,809] [INFO] Found 6/6 markers.
[2024-01-24 11:13:15,845] [INFO] Query marker FASTA was written to GCF_016907015.1_ASM1690701v1_genomic.fna/markers.fasta
[2024-01-24 11:13:15,845] [INFO] Task started: Blastn
[2024-01-24 11:13:15,846] [INFO] Running command: blastn -query GCF_016907015.1_ASM1690701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference/reference_markers.fasta -out GCF_016907015.1_ASM1690701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:16,837] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:16,842] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:16,842] [INFO] Target genome list was writen to GCF_016907015.1_ASM1690701v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:16,862] [INFO] Task started: fastANI
[2024-01-24 11:13:16,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ac175fe-c43c-4ddf-bee1-3750e735d41f/GCF_016907015.1_ASM1690701v1_genomic.fna.gz --refList GCF_016907015.1_ASM1690701v1_genomic.fna/target_genomes.txt --output GCF_016907015.1_ASM1690701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:28,702] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:28,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:28,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:28,718] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:28,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:28,718] [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
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	100.0	1089	1091	95	conclusive
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	89.8564	843	1091	95	below_threshold
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	89.7741	827	1091	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	87.059	816	1091	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	83.0272	743	1091	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	83.0216	705	1091	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	81.8963	692	1091	95	below_threshold
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	81.5208	711	1091	95	below_threshold
Oceanisphaera marina	strain=CGMCC 1.15923	GCA_014643915.1	2017550	2017550	type	True	81.2244	639	1091	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	80.6388	571	1091	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5574	129	1091	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.3409	123	1091	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.2737	115	1091	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2113	161	1091	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.0063	115	1091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:28,720] [INFO] DFAST Taxonomy check result was written to GCF_016907015.1_ASM1690701v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:28,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:28,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:28,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference/checkm_data
[2024-01-24 11:13:28,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:28,758] [INFO] Task started: CheckM
[2024-01-24 11:13:28,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907015.1_ASM1690701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907015.1_ASM1690701v1_genomic.fna/checkm_input GCF_016907015.1_ASM1690701v1_genomic.fna/checkm_result
[2024-01-24 11:14:01,748] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:01,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:01,769] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:01,769] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:01,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907015.1_ASM1690701v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:01,770] [INFO] Task started: Blastn
[2024-01-24 11:14:01,770] [INFO] Running command: blastn -query GCF_016907015.1_ASM1690701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5749a0a8-6b90-483a-8f7a-0bcde253b8e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907015.1_ASM1690701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:03,528] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:03,533] [INFO] Selected 8 target genomes.
[2024-01-24 11:14:03,533] [INFO] Target genome list was writen to GCF_016907015.1_ASM1690701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:03,539] [INFO] Task started: fastANI
[2024-01-24 11:14:03,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ac175fe-c43c-4ddf-bee1-3750e735d41f/GCF_016907015.1_ASM1690701v1_genomic.fna.gz --refList GCF_016907015.1_ASM1690701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907015.1_ASM1690701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:10,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:10,711] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:10,711] [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_016907015.1	s__Oceanisphaera litoralis	100.0	1089	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002936955.1	s__Oceanisphaera arctica	89.7741	827	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018222825.1	s__Oceanisphaera sp018222825	87.617	656	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	87.059	816	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237365.1	s__Zobellella denitrificans	83.0209	705	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_003012775.1	s__Zobellella_C endophytica	83.0136	745	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	82.9448	750	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643915.1	s__Oceanisphaera marina	81.1974	642	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:10,713] [INFO] GTDB search result was written to GCF_016907015.1_ASM1690701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:10,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:10,716] [INFO] DFAST_QC result json was written to GCF_016907015.1_ASM1690701v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:10,717] [INFO] DFAST_QC completed!
[2024-01-24 11:14:10,717] [INFO] Total running time: 0h1m6s