[2024-01-24 12:47:28,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:28,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:28,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference
[2024-01-24 12:47:29,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:29,310] [INFO] Task started: Prodigal
[2024-01-24 12:47:29,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d71b641-96ee-493a-930b-fc3167b9bc83/GCF_009674495.1_ASM967449v1_genomic.fna.gz | prodigal -d GCF_009674495.1_ASM967449v1_genomic.fna/cds.fna -a GCF_009674495.1_ASM967449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:49,606] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:49,606] [INFO] Task started: HMMsearch
[2024-01-24 12:47:49,606] [INFO] Running command: hmmsearch --tblout GCF_009674495.1_ASM967449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference/reference_markers.hmm GCF_009674495.1_ASM967449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:49,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:49,969] [INFO] Found 6/6 markers.
[2024-01-24 12:47:50,020] [INFO] Query marker FASTA was written to GCF_009674495.1_ASM967449v1_genomic.fna/markers.fasta
[2024-01-24 12:47:50,021] [INFO] Task started: Blastn
[2024-01-24 12:47:50,021] [INFO] Running command: blastn -query GCF_009674495.1_ASM967449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference/reference_markers.fasta -out GCF_009674495.1_ASM967449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:51,104] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:51,107] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:51,108] [INFO] Target genome list was writen to GCF_009674495.1_ASM967449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:51,112] [INFO] Task started: fastANI
[2024-01-24 12:47:51,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d71b641-96ee-493a-930b-fc3167b9bc83/GCF_009674495.1_ASM967449v1_genomic.fna.gz --refList GCF_009674495.1_ASM967449v1_genomic.fna/target_genomes.txt --output GCF_009674495.1_ASM967449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:12,742] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:12,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:12,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:12,754] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:48:12,754] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:48:12,754] [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 alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	100.0	2100	2104	95	inconclusive
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	95.0841	1835	2104	95	inconclusive
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	89.4952	1744	2104	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	89.3989	1711	2104	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	89.2248	1728	2104	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	87.7128	1421	2104	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	87.576	1572	2104	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	86.6181	1607	2104	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	86.5094	1532	2104	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	83.4952	1270	2104	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	83.2015	1134	2104	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	83.0893	1127	2104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:12,756] [INFO] DFAST Taxonomy check result was written to GCF_009674495.1_ASM967449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:12,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:12,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:12,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference/checkm_data
[2024-01-24 12:48:12,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:12,822] [INFO] Task started: CheckM
[2024-01-24 12:48:12,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674495.1_ASM967449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674495.1_ASM967449v1_genomic.fna/checkm_input GCF_009674495.1_ASM967449v1_genomic.fna/checkm_result
[2024-01-24 12:49:09,630] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:09,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:09,659] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:09,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:09,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674495.1_ASM967449v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:09,660] [INFO] Task started: Blastn
[2024-01-24 12:49:09,660] [INFO] Running command: blastn -query GCF_009674495.1_ASM967449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93843972-6ca2-4039-a7e7-c60214a1b8a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674495.1_ASM967449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:11,679] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:11,684] [INFO] Selected 13 target genomes.
[2024-01-24 12:49:11,684] [INFO] Target genome list was writen to GCF_009674495.1_ASM967449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:11,732] [INFO] Task started: fastANI
[2024-01-24 12:49:11,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d71b641-96ee-493a-930b-fc3167b9bc83/GCF_009674495.1_ASM967449v1_genomic.fna.gz --refList GCF_009674495.1_ASM967449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674495.1_ASM967449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:34,695] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:34,718] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:34,719] [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_009674495.1	s__Duganella alba	100.0	2100	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	conclusive
GCF_009674565.1	s__Duganella rivi	95.0842	1835	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_009857605.1	s__Duganella levis	89.4882	1745	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857535.1	s__Duganella margarita	89.4277	1707	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.08	98.08	0.91	0.91	2	-
GCF_012849375.1	s__Duganella sp003217375	89.2119	1729	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.22	98.21	0.93	0.93	11	-
GCF_013408245.1	s__Duganella sp013408245	88.9713	1651	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376005.1	s__Duganella sp013376005	87.725	1598	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100205.1	s__Duganella sp900100205	87.6446	1580	2104	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	87.5717	1572	2104	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	87.5544	1434	2104	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	87.5077	1545	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011090165.1	s__Duganella aceris	86.5562	1616	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857445.1	s__Duganella sp009857445	86.4879	1535	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:34,720] [INFO] GTDB search result was written to GCF_009674495.1_ASM967449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:34,721] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:34,725] [INFO] DFAST_QC result json was written to GCF_009674495.1_ASM967449v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:34,725] [INFO] DFAST_QC completed!
[2024-01-24 12:49:34,725] [INFO] Total running time: 0h2m7s