[2024-01-24 15:18:50,997] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:50,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:50,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference
[2024-01-24 15:18:52,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,323] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,323] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb44a8d3-9647-4eef-9c28-c974bdf6f003/GCF_017498065.1_ASM1749806v1_genomic.fna.gz | prodigal -d GCF_017498065.1_ASM1749806v1_genomic.fna/cds.fna -a GCF_017498065.1_ASM1749806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:59,610] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:59,611] [INFO] Task started: HMMsearch
[2024-01-24 15:18:59,611] [INFO] Running command: hmmsearch --tblout GCF_017498065.1_ASM1749806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference/reference_markers.hmm GCF_017498065.1_ASM1749806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:59,908] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:59,910] [INFO] Found 6/6 markers.
[2024-01-24 15:18:59,946] [INFO] Query marker FASTA was written to GCF_017498065.1_ASM1749806v1_genomic.fna/markers.fasta
[2024-01-24 15:18:59,947] [INFO] Task started: Blastn
[2024-01-24 15:18:59,947] [INFO] Running command: blastn -query GCF_017498065.1_ASM1749806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference/reference_markers.fasta -out GCF_017498065.1_ASM1749806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:00,798] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:00,802] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:00,803] [INFO] Target genome list was writen to GCF_017498065.1_ASM1749806v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:00,812] [INFO] Task started: fastANI
[2024-01-24 15:19:00,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb44a8d3-9647-4eef-9c28-c974bdf6f003/GCF_017498065.1_ASM1749806v1_genomic.fna.gz --refList GCF_017498065.1_ASM1749806v1_genomic.fna/target_genomes.txt --output GCF_017498065.1_ASM1749806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:15,081] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:15,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:15,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:15,093] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:15,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:15,094] [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 pacifica	strain=DM8	GCA_017498065.1	2818389	2818389	type	True	100.0	1016	1018	95	conclusive
Oceanisphaera profunda	strain=SM1222	GCA_002157895.1	1416627	1416627	type	True	79.4773	494	1018	95	below_threshold
Oceanisphaera marina	strain=CGMCC 1.15923	GCA_014643915.1	2017550	2017550	type	True	79.0829	436	1018	95	below_threshold
Oceanisphaera avium	strain=AMac2203	GCA_002157875.1	1903694	1903694	type	True	79.047	391	1018	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	78.205	215	1018	95	below_threshold
Oceanisphaera arctica	strain=V1-41	GCA_002936955.1	641510	641510	type	True	78.0704	235	1018	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	78.0236	243	1018	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	77.9934	205	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:15,097] [INFO] DFAST Taxonomy check result was written to GCF_017498065.1_ASM1749806v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:15,098] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:15,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:15,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference/checkm_data
[2024-01-24 15:19:15,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:15,135] [INFO] Task started: CheckM
[2024-01-24 15:19:15,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017498065.1_ASM1749806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017498065.1_ASM1749806v1_genomic.fna/checkm_input GCF_017498065.1_ASM1749806v1_genomic.fna/checkm_result
[2024-01-24 15:19:41,921] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:41,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:41,942] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:41,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:41,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017498065.1_ASM1749806v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:41,943] [INFO] Task started: Blastn
[2024-01-24 15:19:41,943] [INFO] Running command: blastn -query GCF_017498065.1_ASM1749806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20ad3d76-5862-4388-b153-3009bce3d8d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017498065.1_ASM1749806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:43,146] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:43,151] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:43,151] [INFO] Target genome list was writen to GCF_017498065.1_ASM1749806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:43,164] [INFO] Task started: fastANI
[2024-01-24 15:19:43,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb44a8d3-9647-4eef-9c28-c974bdf6f003/GCF_017498065.1_ASM1749806v1_genomic.fna.gz --refList GCF_017498065.1_ASM1749806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017498065.1_ASM1749806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:53,630] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:53,640] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:53,640] [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_017498065.1	s__Oceanisphaera sp017498065	100.0	1016	1018	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_002157895.1	s__Oceanisphaera profunda	79.446	494	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643915.1	s__Oceanisphaera marina	79.1142	433	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157875.1	s__Oceanisphaera avium	79.0508	390	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883865.1	s__Oceanisphaera merdipullorum	78.6733	340	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518835.1	s__Oceanisphaera sp012518835	78.2887	305	1018	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	78.2235	213	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222825.1	s__Oceanisphaera sp018222825	78.1853	189	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002936955.1	s__Oceanisphaera arctica	78.0531	237	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003049725.1	s__Oceanimonas marisflavi	77.5407	131	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381965.1	s__Oceanimonas smirnovii	77.2549	189	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:53,644] [INFO] GTDB search result was written to GCF_017498065.1_ASM1749806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:53,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:53,649] [INFO] DFAST_QC result json was written to GCF_017498065.1_ASM1749806v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:53,649] [INFO] DFAST_QC completed!
[2024-01-24 15:19:53,649] [INFO] Total running time: 0h1m3s