[2024-01-25 20:00:35,695] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:35,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:35,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference
[2024-01-25 20:00:36,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:36,859] [INFO] Task started: Prodigal
[2024-01-25 20:00:36,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cacf296-1467-470b-82e4-f6afe7733fdc/GCF_009857535.1_ASM985753v1_genomic.fna.gz | prodigal -d GCF_009857535.1_ASM985753v1_genomic.fna/cds.fna -a GCF_009857535.1_ASM985753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:54,704] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:54,704] [INFO] Task started: HMMsearch
[2024-01-25 20:00:54,704] [INFO] Running command: hmmsearch --tblout GCF_009857535.1_ASM985753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference/reference_markers.hmm GCF_009857535.1_ASM985753v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:55,005] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:55,006] [INFO] Found 6/6 markers.
[2024-01-25 20:00:55,058] [INFO] Query marker FASTA was written to GCF_009857535.1_ASM985753v1_genomic.fna/markers.fasta
[2024-01-25 20:00:55,059] [INFO] Task started: Blastn
[2024-01-25 20:00:55,059] [INFO] Running command: blastn -query GCF_009857535.1_ASM985753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference/reference_markers.fasta -out GCF_009857535.1_ASM985753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:55,939] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:55,942] [INFO] Selected 12 target genomes.
[2024-01-25 20:00:55,942] [INFO] Target genome list was writen to GCF_009857535.1_ASM985753v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:55,949] [INFO] Task started: fastANI
[2024-01-25 20:00:55,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cacf296-1467-470b-82e4-f6afe7733fdc/GCF_009857535.1_ASM985753v1_genomic.fna.gz --refList GCF_009857535.1_ASM985753v1_genomic.fna/target_genomes.txt --output GCF_009857535.1_ASM985753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:16,801] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:16,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:16,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:16,810] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:16,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:16,811] [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
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	100.0	2105	2108	95	conclusive
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	93.9326	1822	2108	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	93.6447	1865	2108	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	89.4957	1699	2108	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	89.4631	1683	2108	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	87.1497	1458	2108	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	86.8863	1575	2108	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	86.006	1497	2108	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	85.7618	1544	2108	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.8726	1300	2108	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.6792	1110	2108	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	82.5866	1069	2108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:16,812] [INFO] DFAST Taxonomy check result was written to GCF_009857535.1_ASM985753v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:16,813] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:16,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:16,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference/checkm_data
[2024-01-25 20:01:16,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:16,872] [INFO] Task started: CheckM
[2024-01-25 20:01:16,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857535.1_ASM985753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857535.1_ASM985753v1_genomic.fna/checkm_input GCF_009857535.1_ASM985753v1_genomic.fna/checkm_result
[2024-01-25 20:02:06,532] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:06,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:06,562] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:06,562] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:06,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857535.1_ASM985753v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:06,564] [INFO] Task started: Blastn
[2024-01-25 20:02:06,564] [INFO] Running command: blastn -query GCF_009857535.1_ASM985753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4db04ab2-4367-4026-859a-eae4625c37ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857535.1_ASM985753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:08,346] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:08,349] [INFO] Selected 10 target genomes.
[2024-01-25 20:02:08,349] [INFO] Target genome list was writen to GCF_009857535.1_ASM985753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:08,360] [INFO] Task started: fastANI
[2024-01-25 20:02:08,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cacf296-1467-470b-82e4-f6afe7733fdc/GCF_009857535.1_ASM985753v1_genomic.fna.gz --refList GCF_009857535.1_ASM985753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857535.1_ASM985753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:26,212] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:26,220] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:26,220] [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_009857535.1	s__Duganella margarita	100.0	2105	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.08	98.08	0.91	0.91	2	conclusive
GCF_009857605.1	s__Duganella levis	93.9278	1823	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849375.1	s__Duganella sp003217375	93.6344	1866	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.22	98.21	0.93	0.93	11	-
GCF_009674495.1	s__Duganella alba	89.499	1698	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_009674565.1	s__Duganella rivi	89.4558	1686	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_013408245.1	s__Duganella sp013408245	89.072	1694	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857495.1	s__Duganella sp009857495	87.1161	1452	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.63	98.63	0.91	0.91	2	-
GCF_900109645.1	s__Duganella sp900109645	86.9544	1526	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009720825.1	s__Duganella radicis	86.8873	1574	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019219065.1	s__Duganella sp019219065	86.7556	1554	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:26,221] [INFO] GTDB search result was written to GCF_009857535.1_ASM985753v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:26,222] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:26,224] [INFO] DFAST_QC result json was written to GCF_009857535.1_ASM985753v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:26,224] [INFO] DFAST_QC completed!
[2024-01-25 20:02:26,224] [INFO] Total running time: 0h1m51s