[2024-01-25 17:50:35,364] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:35,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:35,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference
[2024-01-25 17:50:36,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:36,468] [INFO] Task started: Prodigal
[2024-01-25 17:50:36,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg631830ea-86ec-49c9-a15b-23cabbd91db2/GCF_014651395.1_ASM1465139v1_genomic.fna.gz | prodigal -d GCF_014651395.1_ASM1465139v1_genomic.fna/cds.fna -a GCF_014651395.1_ASM1465139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:55,769] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:55,769] [INFO] Task started: HMMsearch
[2024-01-25 17:50:55,769] [INFO] Running command: hmmsearch --tblout GCF_014651395.1_ASM1465139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference/reference_markers.hmm GCF_014651395.1_ASM1465139v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:56,060] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:56,061] [INFO] Found 6/6 markers.
[2024-01-25 17:50:56,112] [INFO] Query marker FASTA was written to GCF_014651395.1_ASM1465139v1_genomic.fna/markers.fasta
[2024-01-25 17:50:56,112] [INFO] Task started: Blastn
[2024-01-25 17:50:56,112] [INFO] Running command: blastn -query GCF_014651395.1_ASM1465139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference/reference_markers.fasta -out GCF_014651395.1_ASM1465139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:57,004] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:57,007] [INFO] Selected 13 target genomes.
[2024-01-25 17:50:57,007] [INFO] Target genome list was writen to GCF_014651395.1_ASM1465139v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:57,015] [INFO] Task started: fastANI
[2024-01-25 17:50:57,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg631830ea-86ec-49c9-a15b-23cabbd91db2/GCF_014651395.1_ASM1465139v1_genomic.fna.gz --refList GCF_014651395.1_ASM1465139v1_genomic.fna/target_genomes.txt --output GCF_014651395.1_ASM1465139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:18,326] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:18,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:18,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:18,336] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:51:18,336] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:18,336] [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
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	100.0	2231	2237	95	conclusive
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	99.9918	2232	2237	95	conclusive
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	87.5877	1741	2237	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	87.5726	1746	2237	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	87.5109	1754	2237	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	87.2688	1771	2237	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	84.9389	1455	2237	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	83.2964	1362	2237	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.1107	970	2237	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.0022	1158	2237	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	80.6761	971	2237	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.4152	849	2237	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.1717	918	2237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:18,337] [INFO] DFAST Taxonomy check result was written to GCF_014651395.1_ASM1465139v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:18,339] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:18,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:18,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference/checkm_data
[2024-01-25 17:51:18,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:18,410] [INFO] Task started: CheckM
[2024-01-25 17:51:18,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651395.1_ASM1465139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651395.1_ASM1465139v1_genomic.fna/checkm_input GCF_014651395.1_ASM1465139v1_genomic.fna/checkm_result
[2024-01-25 17:52:23,291] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:23,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:23,316] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:23,316] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:23,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651395.1_ASM1465139v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:23,317] [INFO] Task started: Blastn
[2024-01-25 17:52:23,317] [INFO] Running command: blastn -query GCF_014651395.1_ASM1465139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7690991-849f-4315-8230-7d6366e39e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651395.1_ASM1465139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:25,166] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:25,169] [INFO] Selected 8 target genomes.
[2024-01-25 17:52:25,169] [INFO] Target genome list was writen to GCF_014651395.1_ASM1465139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:25,183] [INFO] Task started: fastANI
[2024-01-25 17:52:25,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg631830ea-86ec-49c9-a15b-23cabbd91db2/GCF_014651395.1_ASM1465139v1_genomic.fna.gz --refList GCF_014651395.1_ASM1465139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651395.1_ASM1465139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:40,460] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:40,466] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:40,466] [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_009727155.1	s__Pseudoduganella dura	99.9918	2232	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004322755.1	s__Pseudoduganella albidiflava	87.5916	1742	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192225.1	s__Pseudoduganella umbonata	87.501	1756	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	87.2716	1770	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830495.1	s__Pseudoduganella flava	85.1756	1537	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830455.1	s__Pseudoduganella lurida	84.9116	1459	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454505.1	s__Pseudoduganella sp002454505	84.6756	1325	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720835.1	s__Pseudoduganella buxea	83.3575	1335	2237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:40,467] [INFO] GTDB search result was written to GCF_014651395.1_ASM1465139v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:40,468] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:40,470] [INFO] DFAST_QC result json was written to GCF_014651395.1_ASM1465139v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:40,471] [INFO] DFAST_QC completed!
[2024-01-25 17:52:40,471] [INFO] Total running time: 0h2m5s