[2024-01-24 12:44:52,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,394] [INFO] DQC Reference Directory: /var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference
[2024-01-24 12:44:53,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,781] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,782] [INFO] Running command: gunzip -c /var/lib/cwl/stgf22a7c6e-4fb0-4ca5-ac5f-70fc585c609d/GCF_024764835.1_ASM2476483v1_genomic.fna.gz | prodigal -d GCF_024764835.1_ASM2476483v1_genomic.fna/cds.fna -a GCF_024764835.1_ASM2476483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:07,836] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:07,837] [INFO] Task started: HMMsearch
[2024-01-24 12:45:07,837] [INFO] Running command: hmmsearch --tblout GCF_024764835.1_ASM2476483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference/reference_markers.hmm GCF_024764835.1_ASM2476483v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:08,121] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:08,122] [INFO] Found 6/6 markers.
[2024-01-24 12:45:08,164] [INFO] Query marker FASTA was written to GCF_024764835.1_ASM2476483v1_genomic.fna/markers.fasta
[2024-01-24 12:45:08,164] [INFO] Task started: Blastn
[2024-01-24 12:45:08,164] [INFO] Running command: blastn -query GCF_024764835.1_ASM2476483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference/reference_markers.fasta -out GCF_024764835.1_ASM2476483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:09,103] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:09,108] [INFO] Selected 26 target genomes.
[2024-01-24 12:45:09,108] [INFO] Target genome list was writen to GCF_024764835.1_ASM2476483v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:09,119] [INFO] Task started: fastANI
[2024-01-24 12:45:09,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22a7c6e-4fb0-4ca5-ac5f-70fc585c609d/GCF_024764835.1_ASM2476483v1_genomic.fna.gz --refList GCF_024764835.1_ASM2476483v1_genomic.fna/target_genomes.txt --output GCF_024764835.1_ASM2476483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:34,794] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:34,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:34,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:34,821] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:34,821] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:34,821] [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
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.7102	883	1598	95	below_threshold
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	81.6997	920	1598	95	below_threshold
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	81.685	867	1598	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.6822	890	1598	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.634	906	1598	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	81.5937	897	1598	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	81.5869	878	1598	95	below_threshold
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	81.5457	839	1598	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	81.4508	926	1598	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	81.4312	875	1598	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	81.3928	836	1598	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	81.3616	872	1598	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.3338	885	1598	95	below_threshold
Enterobacter soli	strain=ATCC BAA-2102	GCA_001654845.1	885040	885040	type	True	81.2537	873	1598	95	below_threshold
Enterobacter soli		GCA_900185935.1	885040	885040	type	True	81.2534	870	1598	95	below_threshold
Enterobacter oligotrophicus	strain=CCA6	GCA_009176645.1	2478464	2478464	type	True	81.2277	875	1598	95	below_threshold
Kluyvera cryocrescens	strain=NBRC 102467	GCA_001571285.1	580	580	type	True	81.0617	874	1598	95	below_threshold
Klebsiella spallanzanii		GCA_902158555.1	2587528	2587528	type	True	80.9538	833	1598	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	80.926	851	1598	95	below_threshold
Kluyvera intermedia	strain=NCTC12125	GCA_900635475.1	61648	61648	suspected-type	True	80.9098	821	1598	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	80.8903	838	1598	95	below_threshold
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	80.853	786	1598	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	80.8374	831	1598	95	below_threshold
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	80.8064	844	1598	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.7865	829	1598	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	80.746	805	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:34,823] [INFO] DFAST Taxonomy check result was written to GCF_024764835.1_ASM2476483v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:34,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:34,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:34,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference/checkm_data
[2024-01-24 12:45:34,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:34,875] [INFO] Task started: CheckM
[2024-01-24 12:45:34,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024764835.1_ASM2476483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024764835.1_ASM2476483v1_genomic.fna/checkm_input GCF_024764835.1_ASM2476483v1_genomic.fna/checkm_result
[2024-01-24 12:46:17,327] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:17,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:17,352] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:17,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:17,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024764835.1_ASM2476483v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:17,353] [INFO] Task started: Blastn
[2024-01-24 12:46:17,353] [INFO] Running command: blastn -query GCF_024764835.1_ASM2476483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3787561-27e5-42c0-8449-e0f9a9e30207/dqc_reference/reference_markers_gtdb.fasta -out GCF_024764835.1_ASM2476483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:18,802] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:18,807] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:18,807] [INFO] Target genome list was writen to GCF_024764835.1_ASM2476483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:18,813] [INFO] Task started: fastANI
[2024-01-24 12:46:18,813] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22a7c6e-4fb0-4ca5-ac5f-70fc585c609d/GCF_024764835.1_ASM2476483v1_genomic.fna.gz --refList GCF_024764835.1_ASM2476483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024764835.1_ASM2476483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:27,893] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:27,905] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:27,905] [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_902706235.1	s__Scandinavium sp902706235	95.1903	1347	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902706205.1	s__Scandinavium sp902706205	94.2807	1347	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003935895.2	s__Scandinavium goeteborgense	93.038	1252	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	97.59	96.23	0.90	0.88	4	-
GCF_900215375.1	s__Scandinavium sp900215375	85.1397	1148	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470465.1	s__Scandinavium sp002470465	84.8393	1092	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009668205.1	s__Scandinavium sp009668205	84.0657	1074	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115925.1	s__Lelliottia nimipressuralis	81.6917	921	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.29	98.00	0.93	0.92	11	-
GCA_901456055.1	s__Phytobacter ursingii	80.374	769	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:27,909] [INFO] GTDB search result was written to GCF_024764835.1_ASM2476483v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:27,909] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:27,915] [INFO] DFAST_QC result json was written to GCF_024764835.1_ASM2476483v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:27,916] [INFO] DFAST_QC completed!
[2024-01-24 12:46:27,916] [INFO] Total running time: 0h1m36s