[2024-01-24 11:58:56,954] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:56,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:56,962] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference
[2024-01-24 11:58:58,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,396] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg59e5816e-81e5-4f10-8c09-c2ce4509f789/GCF_016746085.1_ASM1674608v1_genomic.fna.gz | prodigal -d GCF_016746085.1_ASM1674608v1_genomic.fna/cds.fna -a GCF_016746085.1_ASM1674608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:11,430] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:11,430] [INFO] Task started: HMMsearch
[2024-01-24 11:59:11,430] [INFO] Running command: hmmsearch --tblout GCF_016746085.1_ASM1674608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference/reference_markers.hmm GCF_016746085.1_ASM1674608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:11,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:11,726] [INFO] Found 6/6 markers.
[2024-01-24 11:59:11,761] [INFO] Query marker FASTA was written to GCF_016746085.1_ASM1674608v1_genomic.fna/markers.fasta
[2024-01-24 11:59:11,762] [INFO] Task started: Blastn
[2024-01-24 11:59:11,762] [INFO] Running command: blastn -query GCF_016746085.1_ASM1674608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference/reference_markers.fasta -out GCF_016746085.1_ASM1674608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:12,714] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:12,720] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:12,721] [INFO] Target genome list was writen to GCF_016746085.1_ASM1674608v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:12,727] [INFO] Task started: fastANI
[2024-01-24 11:59:12,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e5816e-81e5-4f10-8c09-c2ce4509f789/GCF_016746085.1_ASM1674608v1_genomic.fna.gz --refList GCF_016746085.1_ASM1674608v1_genomic.fna/target_genomes.txt --output GCF_016746085.1_ASM1674608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:24,063] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:24,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:24,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:24,077] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:24,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:24,077] [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
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	92.16	1031	1392	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	89.4664	1070	1392	95	below_threshold
Zobellella taiwanensis	strain=JCM 13381	GCA_003012795.1	347535	347535	type	True	87.4698	940	1392	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	83.0948	823	1392	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	82.9397	743	1392	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	82.6327	754	1392	95	below_threshold
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	82.6147	742	1392	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	82.6137	739	1392	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.0025	302	1392	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.7942	224	1392	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.7842	234	1392	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6412	234	1392	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.5748	202	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:24,079] [INFO] DFAST Taxonomy check result was written to GCF_016746085.1_ASM1674608v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:24,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:24,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:24,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference/checkm_data
[2024-01-24 11:59:24,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:24,145] [INFO] Task started: CheckM
[2024-01-24 11:59:24,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016746085.1_ASM1674608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016746085.1_ASM1674608v1_genomic.fna/checkm_input GCF_016746085.1_ASM1674608v1_genomic.fna/checkm_result
[2024-01-24 12:00:02,037] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:02,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:02,057] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:02,057] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:02,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016746085.1_ASM1674608v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:02,058] [INFO] Task started: Blastn
[2024-01-24 12:00:02,058] [INFO] Running command: blastn -query GCF_016746085.1_ASM1674608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5d5667f-330c-46a1-a5c2-70260b23eaf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016746085.1_ASM1674608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:03,652] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:03,656] [INFO] Selected 8 target genomes.
[2024-01-24 12:00:03,656] [INFO] Target genome list was writen to GCF_016746085.1_ASM1674608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:03,662] [INFO] Task started: fastANI
[2024-01-24 12:00:03,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e5816e-81e5-4f10-8c09-c2ce4509f789/GCF_016746085.1_ASM1674608v1_genomic.fna.gz --refList GCF_016746085.1_ASM1674608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016746085.1_ASM1674608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:11,797] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:11,806] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:11,807] [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_016746085.1	s__CGMCC-1-18722 sp016746085	100.0	1391	1392	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	conclusive
GCF_002237365.1	s__Zobellella denitrificans	92.1544	1033	1392	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	89.4577	1071	1392	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_003012795.1	s__Zobellella_D taiwanensis	87.4754	940	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	83.0852	825	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907015.1	s__Oceanisphaera litoralis	82.9326	743	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049725.1	s__Oceanimonas marisflavi	82.6105	740	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075035.1	s__Zobellella_A maritima	81.5976	741	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:11,808] [INFO] GTDB search result was written to GCF_016746085.1_ASM1674608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:11,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:11,814] [INFO] DFAST_QC result json was written to GCF_016746085.1_ASM1674608v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:11,814] [INFO] DFAST_QC completed!
[2024-01-24 12:00:11,814] [INFO] Total running time: 0h1m15s