[2024-01-24 12:36:58,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,582] [INFO] DQC Reference Directory: /var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference
[2024-01-24 12:36:59,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,973] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg1486de79-bd43-4439-b832-9cb6640c94b8/GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna.gz | prodigal -d GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/cds.fna -a GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:14,671] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:14,671] [INFO] Task started: HMMsearch
[2024-01-24 12:37:14,671] [INFO] Running command: hmmsearch --tblout GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference/reference_markers.hmm GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:15,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:15,040] [INFO] Found 6/6 markers.
[2024-01-24 12:37:15,098] [INFO] Query marker FASTA was written to GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/markers.fasta
[2024-01-24 12:37:15,099] [INFO] Task started: Blastn
[2024-01-24 12:37:15,099] [INFO] Running command: blastn -query GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/markers.fasta -db /var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference/reference_markers.fasta -out GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:16,065] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:16,068] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:16,068] [INFO] Target genome list was writen to GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/target_genomes.txt
[2024-01-24 12:37:16,076] [INFO] Task started: fastANI
[2024-01-24 12:37:16,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg1486de79-bd43-4439-b832-9cb6640c94b8/GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna.gz --refList GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/target_genomes.txt --output GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:29,437] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:29,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:29,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:29,451] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:29,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:29,452] [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 pseudosacchari	strain=JM-387	GCA_900184035.1	1646340	1646340	type	True	100.0	1635	1637	95	conclusive
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	94.8994	1487	1637	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	94.8803	1492	1637	95	below_threshold
Kosakonia quasisacchari	strain=WCHEs120001	GCA_004331415.1	2529380	2529380	type	True	92.7184	1481	1637	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	84.9744	1293	1637	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	84.3787	1224	1637	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	84.063	1149	1637	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.3883	904	1637	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.3752	910	1637	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.3576	884	1637	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	80.9702	851	1637	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	80.9646	844	1637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:29,454] [INFO] DFAST Taxonomy check result was written to GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/tc_result.tsv
[2024-01-24 12:37:29,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:29,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:29,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference/checkm_data
[2024-01-24 12:37:29,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:29,508] [INFO] Task started: CheckM
[2024-01-24 12:37:29,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/checkm_input GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/checkm_result
[2024-01-24 12:38:14,818] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:14,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:14,844] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:14,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:14,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/markers.fasta)
[2024-01-24 12:38:14,845] [INFO] Task started: Blastn
[2024-01-24 12:38:14,846] [INFO] Running command: blastn -query GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/markers.fasta -db /var/lib/cwl/stgd54c79ed-93c5-43c2-b58d-545bb5cc0d06/dqc_reference/reference_markers_gtdb.fasta -out GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:16,212] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:16,217] [INFO] Selected 7 target genomes.
[2024-01-24 12:38:16,218] [INFO] Target genome list was writen to GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:16,229] [INFO] Task started: fastANI
[2024-01-24 12:38:16,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg1486de79-bd43-4439-b832-9cb6640c94b8/GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna.gz --refList GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/target_genomes_gtdb.txt --output GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:25,442] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:25,455] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:25,456] [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_900184035.1	s__Kosakonia pseudosacchari	100.0	1635	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.43	98.39	0.94	0.93	3	conclusive
GCF_000300455.3	s__Kosakonia sacchari	94.8803	1492	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.35	95.81	0.96	0.92	5	-
GCF_000410515.1	s__Kosakonia sp000410515	94.0269	1512	1637	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	92.7184	1481	1637	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	86.338	1213	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280495.2	s__Kosakonia radicincitans	84.9864	1274	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_001975225.1	s__Kosakonia cowanii	84.0618	1150	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,458] [INFO] GTDB search result was written to GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:25,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:25,463] [INFO] DFAST_QC result json was written to GCF_900184035.1_Kosakonia_pseudosacchari_JM-387_T_genomic.fna/dqc_result.json
[2024-01-24 12:38:25,463] [INFO] DFAST_QC completed!
[2024-01-24 12:38:25,464] [INFO] Total running time: 0h1m27s