[2024-01-24 13:13:38,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:38,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:38,279] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference
[2024-01-24 13:13:39,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:39,599] [INFO] Task started: Prodigal
[2024-01-24 13:13:39,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg8884aa08-4435-451d-b437-f5be62e8379d/GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna.gz | prodigal -d GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/cds.fna -a GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:51,541] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:51,542] [INFO] Task started: HMMsearch
[2024-01-24 13:13:51,542] [INFO] Running command: hmmsearch --tblout GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference/reference_markers.hmm GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:51,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:51,855] [INFO] Found 6/6 markers.
[2024-01-24 13:13:51,910] [INFO] Query marker FASTA was written to GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/markers.fasta
[2024-01-24 13:13:51,910] [INFO] Task started: Blastn
[2024-01-24 13:13:51,910] [INFO] Running command: blastn -query GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference/reference_markers.fasta -out GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:52,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:52,823] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:52,824] [INFO] Target genome list was writen to GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:52,828] [INFO] Task started: fastANI
[2024-01-24 13:13:52,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg8884aa08-4435-451d-b437-f5be62e8379d/GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna.gz --refList GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:03,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:03,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:03,586] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:03,587] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:03,587] [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
Hafnia paralvei	strain=ATCC 29927	GCA_001655005.1	546367	546367	type	True	100.0	1573	1575	95	conclusive
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	99.077	1402	1575	95	conclusive
Hafnia alvei	strain=ATCC 13337	GCA_003668715.1	569	569	type	True	84.2861	1078	1575	95	below_threshold
Hafnia alvei	strain=ATCC 13337	GCA_000735375.1	569	569	type	True	84.2676	1064	1575	95	below_threshold
Obesumbacterium proteus	strain=ATCC 12841	GCA_001655035.1	82983	82983	type	True	84.1762	1038	1575	95	below_threshold
Obesumbacterium proteus	strain=DSM 2777	GCA_001586165.1	82983	82983	type	True	84.1387	1086	1575	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.6674	304	1575	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.5254	314	1575	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.5163	305	1575	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	78.4039	291	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,589] [INFO] DFAST Taxonomy check result was written to GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:03,589] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:03,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:03,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference/checkm_data
[2024-01-24 13:14:03,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:03,636] [INFO] Task started: CheckM
[2024-01-24 13:14:03,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/checkm_input GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/checkm_result
[2024-01-24 13:14:42,098] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:42,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:42,116] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:42,117] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:42,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-24 13:14:42,117] [INFO] Task started: Blastn
[2024-01-24 13:14:42,117] [INFO] Running command: blastn -query GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a45c33-6682-48a7-8f29-c78db316db7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:43,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:43,393] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:43,394] [INFO] Target genome list was writen to GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:43,402] [INFO] Task started: fastANI
[2024-01-24 13:14:43,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg8884aa08-4435-451d-b437-f5be62e8379d/GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna.gz --refList GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:54,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:54,285] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:54,285] [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_001655005.1	s__Hafnia paralvei	100.0	1573	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.49	95.65	0.88	0.84	34	conclusive
GCF_000735375.1	s__Hafnia alvei	84.2681	1064	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	97.59	95.60	0.91	0.87	31	-
GCF_001586165.1	s__Hafnia proteus	84.1384	1086	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	-
GCF_900095695.1	s__Hafnia alvei_B	83.9799	1067	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001112925.1	s__Yersinia nurmii	78.6008	303	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654915.1	s__Buttiauxella ferragutiae	78.5539	293	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	99.06	98.93	0.93	0.91	3	-
GCF_015644585.1	s__Rahnella laticis	78.5318	301	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_001571285.1	s__Kluyvera cryocrescens	78.5218	307	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.35	99.12	0.95	0.93	4	-
GCF_003363015.1	s__Enterobacillus tribolii	78.4866	385	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017832355.1	s__Serratia sp017832355	78.4239	338	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900079995.3	s__Citrobacter europaeus	78.2706	266	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:54,287] [INFO] GTDB search result was written to GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:54,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:54,291] [INFO] DFAST_QC result json was written to GCF_001655005.1_Hpa29927_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-24 13:14:54,291] [INFO] DFAST_QC completed!
[2024-01-24 13:14:54,291] [INFO] Total running time: 0h1m16s