[2024-01-24 13:37:04,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:04,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:04,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference
[2024-01-24 13:37:06,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,269] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg23bf1cc6-d422-4df7-a7a6-c2d7a68f1f84/GCF_012849375.1_ASM1284937v1_genomic.fna.gz | prodigal -d GCF_012849375.1_ASM1284937v1_genomic.fna/cds.fna -a GCF_012849375.1_ASM1284937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:28,805] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:28,805] [INFO] Task started: HMMsearch
[2024-01-24 13:37:28,806] [INFO] Running command: hmmsearch --tblout GCF_012849375.1_ASM1284937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference/reference_markers.hmm GCF_012849375.1_ASM1284937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:29,264] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:29,266] [INFO] Found 6/6 markers.
[2024-01-24 13:37:29,321] [INFO] Query marker FASTA was written to GCF_012849375.1_ASM1284937v1_genomic.fna/markers.fasta
[2024-01-24 13:37:29,322] [INFO] Task started: Blastn
[2024-01-24 13:37:29,322] [INFO] Running command: blastn -query GCF_012849375.1_ASM1284937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference/reference_markers.fasta -out GCF_012849375.1_ASM1284937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:30,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:30,382] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:30,382] [INFO] Target genome list was writen to GCF_012849375.1_ASM1284937v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:30,388] [INFO] Task started: fastANI
[2024-01-24 13:37:30,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg23bf1cc6-d422-4df7-a7a6-c2d7a68f1f84/GCF_012849375.1_ASM1284937v1_genomic.fna.gz --refList GCF_012849375.1_ASM1284937v1_genomic.fna/target_genomes.txt --output GCF_012849375.1_ASM1284937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:48,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:48,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:48,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:48,412] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:48,413] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:48,413] [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 dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	100.0	2177	2177	95	conclusive
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	94.3299	1867	2177	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	93.652	1848	2177	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	89.1915	1731	2177	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	89.1406	1723	2177	95	below_threshold
Duganella guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	86.3676	1631	2177	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	85.3385	1584	2177	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.8183	1268	2177	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.4283	1078	2177	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	82.1884	1079	2177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:48,414] [INFO] DFAST Taxonomy check result was written to GCF_012849375.1_ASM1284937v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:48,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:48,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:48,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference/checkm_data
[2024-01-24 13:37:48,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:48,482] [INFO] Task started: CheckM
[2024-01-24 13:37:48,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012849375.1_ASM1284937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012849375.1_ASM1284937v1_genomic.fna/checkm_input GCF_012849375.1_ASM1284937v1_genomic.fna/checkm_result
[2024-01-24 13:38:49,623] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:49,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:49,650] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:49,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:49,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012849375.1_ASM1284937v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:49,651] [INFO] Task started: Blastn
[2024-01-24 13:38:49,651] [INFO] Running command: blastn -query GCF_012849375.1_ASM1284937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19148101-70b9-4b6f-abbc-c697648b7824/dqc_reference/reference_markers_gtdb.fasta -out GCF_012849375.1_ASM1284937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:51,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:51,573] [INFO] Selected 7 target genomes.
[2024-01-24 13:38:51,574] [INFO] Target genome list was writen to GCF_012849375.1_ASM1284937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:51,586] [INFO] Task started: fastANI
[2024-01-24 13:38:51,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg23bf1cc6-d422-4df7-a7a6-c2d7a68f1f84/GCF_012849375.1_ASM1284937v1_genomic.fna.gz --refList GCF_012849375.1_ASM1284937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012849375.1_ASM1284937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:05,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:05,059] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:05,060] [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_012849375.1	s__Duganella sp003217375	100.0	2177	2177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.22	98.21	0.93	0.93	11	conclusive
GCF_009857605.1	s__Duganella levis	94.3322	1867	2177	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	93.652	1848	2177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.08	98.08	0.91	0.91	2	-
GCF_009674565.1	s__Duganella rivi	89.1594	1735	2177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	89.1235	1726	2177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_900109645.1	s__Duganella sp900109645	86.577	1573	2177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009674535.1	s__Duganella sp009674535	86.3706	1631	2177	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 13:39:05,061] [INFO] GTDB search result was written to GCF_012849375.1_ASM1284937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:05,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:05,067] [INFO] DFAST_QC result json was written to GCF_012849375.1_ASM1284937v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:05,067] [INFO] DFAST_QC completed!
[2024-01-24 13:39:05,067] [INFO] Total running time: 0h2m0s