[2024-01-25 18:16:35,809] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:35,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:35,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference
[2024-01-25 18:16:36,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:36,954] [INFO] Task started: Prodigal
[2024-01-25 18:16:36,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg36ab3337-3920-49a5-b4ab-56a4806ddf33/GCF_000300455.3_ASM30045v4_genomic.fna.gz | prodigal -d GCF_000300455.3_ASM30045v4_genomic.fna/cds.fna -a GCF_000300455.3_ASM30045v4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:49,317] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:49,317] [INFO] Task started: HMMsearch
[2024-01-25 18:16:49,317] [INFO] Running command: hmmsearch --tblout GCF_000300455.3_ASM30045v4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference/reference_markers.hmm GCF_000300455.3_ASM30045v4_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:49,608] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:49,609] [INFO] Found 6/6 markers.
[2024-01-25 18:16:49,648] [INFO] Query marker FASTA was written to GCF_000300455.3_ASM30045v4_genomic.fna/markers.fasta
[2024-01-25 18:16:49,648] [INFO] Task started: Blastn
[2024-01-25 18:16:49,648] [INFO] Running command: blastn -query GCF_000300455.3_ASM30045v4_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference/reference_markers.fasta -out GCF_000300455.3_ASM30045v4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:50,525] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:50,535] [INFO] Selected 13 target genomes.
[2024-01-25 18:16:50,536] [INFO] Target genome list was writen to GCF_000300455.3_ASM30045v4_genomic.fna/target_genomes.txt
[2024-01-25 18:16:50,553] [INFO] Task started: fastANI
[2024-01-25 18:16:50,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ab3337-3920-49a5-b4ab-56a4806ddf33/GCF_000300455.3_ASM30045v4_genomic.fna.gz --refList GCF_000300455.3_ASM30045v4_genomic.fna/target_genomes.txt --output GCF_000300455.3_ASM30045v4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:05,378] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:05,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:05,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:05,387] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:17:05,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:05,387] [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
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	100.0	1633	1634	95	conclusive
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	99.9747	1604	1634	95	conclusive
Kosakonia pseudosacchari	strain=JM-387	GCA_900184035.1	1646340	1646340	type	True	94.8645	1489	1634	95	below_threshold
Kosakonia quasisacchari	strain=WCHEs120001	GCA_004331415.1	2529380	2529380	type	True	93.2101	1496	1634	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	85.2004	1272	1634	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	84.2784	1215	1634	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	84.1471	1155	1634	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.5042	902	1634	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.4689	900	1634	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.4132	883	1634	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.3526	886	1634	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	81.0968	832	1634	95	below_threshold
Raoultella electrica	strain=DSM 102253	GCA_006711645.1	1259973	1259973	type	True	80.957	847	1634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:05,392] [INFO] DFAST Taxonomy check result was written to GCF_000300455.3_ASM30045v4_genomic.fna/tc_result.tsv
[2024-01-25 18:17:05,393] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:05,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:05,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference/checkm_data
[2024-01-25 18:17:05,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:05,448] [INFO] Task started: CheckM
[2024-01-25 18:17:05,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000300455.3_ASM30045v4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000300455.3_ASM30045v4_genomic.fna/checkm_input GCF_000300455.3_ASM30045v4_genomic.fna/checkm_result
[2024-01-25 18:17:43,899] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:43,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:43,937] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:43,937] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:43,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000300455.3_ASM30045v4_genomic.fna/markers.fasta)
[2024-01-25 18:17:43,938] [INFO] Task started: Blastn
[2024-01-25 18:17:43,938] [INFO] Running command: blastn -query GCF_000300455.3_ASM30045v4_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4eee9b8-7287-44f8-bede-6f06b9511db5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000300455.3_ASM30045v4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:45,367] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:45,370] [INFO] Selected 6 target genomes.
[2024-01-25 18:17:45,371] [INFO] Target genome list was writen to GCF_000300455.3_ASM30045v4_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:45,385] [INFO] Task started: fastANI
[2024-01-25 18:17:45,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ab3337-3920-49a5-b4ab-56a4806ddf33/GCF_000300455.3_ASM30045v4_genomic.fna.gz --refList GCF_000300455.3_ASM30045v4_genomic.fna/target_genomes_gtdb.txt --output GCF_000300455.3_ASM30045v4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:53,392] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:53,397] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:53,397] [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_000300455.3	s__Kosakonia sacchari	100.0	1633	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.35	95.81	0.96	0.92	5	conclusive
GCF_900184035.1	s__Kosakonia pseudosacchari	94.8645	1489	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.43	98.39	0.94	0.93	3	-
GCF_000410515.1	s__Kosakonia sp000410515	94.5609	1517	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.63	98.59	0.96	0.95	5	-
GCF_004331415.1	s__Kosakonia quasisacchari	93.2101	1496	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814905.1	s__Kosakonia sp000814905	86.2137	1200	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975225.1	s__Kosakonia cowanii	84.1554	1154	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:53,398] [INFO] GTDB search result was written to GCF_000300455.3_ASM30045v4_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:53,399] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:53,401] [INFO] DFAST_QC result json was written to GCF_000300455.3_ASM30045v4_genomic.fna/dqc_result.json
[2024-01-25 18:17:53,402] [INFO] DFAST_QC completed!
[2024-01-25 18:17:53,402] [INFO] Total running time: 0h1m18s