[2024-01-24 11:27:04,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,596] [INFO] DQC Reference Directory: /var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference
[2024-01-24 11:27:05,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,812] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4eceed2-795f-4203-80b8-944f2cf44d46/GCF_019048105.1_ASM1904810v1_genomic.fna.gz | prodigal -d GCF_019048105.1_ASM1904810v1_genomic.fna/cds.fna -a GCF_019048105.1_ASM1904810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:15,957] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:15,958] [INFO] Task started: HMMsearch
[2024-01-24 11:27:15,958] [INFO] Running command: hmmsearch --tblout GCF_019048105.1_ASM1904810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference/reference_markers.hmm GCF_019048105.1_ASM1904810v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:16,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:16,232] [INFO] Found 6/6 markers.
[2024-01-24 11:27:16,270] [INFO] Query marker FASTA was written to GCF_019048105.1_ASM1904810v1_genomic.fna/markers.fasta
[2024-01-24 11:27:16,270] [INFO] Task started: Blastn
[2024-01-24 11:27:16,270] [INFO] Running command: blastn -query GCF_019048105.1_ASM1904810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference/reference_markers.fasta -out GCF_019048105.1_ASM1904810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:16,996] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:16,999] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:17,000] [INFO] Target genome list was writen to GCF_019048105.1_ASM1904810v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:17,019] [INFO] Task started: fastANI
[2024-01-24 11:27:17,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4eceed2-795f-4203-80b8-944f2cf44d46/GCF_019048105.1_ASM1904810v1_genomic.fna.gz --refList GCF_019048105.1_ASM1904810v1_genomic.fna/target_genomes.txt --output GCF_019048105.1_ASM1904810v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:31,489] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:31,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:31,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:31,507] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:31,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:31,507] [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
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	100.0	1544	1546	95	conclusive
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	91.3843	1230	1546	95	below_threshold
Providencia vermicola	strain=DSM 17385	GCA_020381325.1	333965	333965	suspected-type	True	83.2122	970	1546	95	below_threshold
Providencia heimbachae	strain=NCTC12003	GCA_900475855.1	333962	333962	type	True	81.4089	856	1546	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	81.2981	694	1546	95	below_threshold
Providencia heimbachae	strain=ATCC 35613	GCA_001655055.1	333962	333962	type	True	81.2423	849	1546	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	81.1916	693	1546	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	81.0945	680	1546	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	80.4427	647	1546	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	80.0468	616	1546	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	79.5408	89	1546	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	78.8381	127	1546	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	78.3775	163	1546	95	below_threshold
Proteus terrae subsp. cibarius	strain=JCM 30699	GCA_003144495.1	626774	1574161	type	True	78.3202	297	1546	95	below_threshold
Proteus terrae	strain=LMG 28659	GCA_003144325.1	1574161	1574161	type	True	78.1288	286	1546	95	below_threshold
Proteus alimentorum	strain=08MAS0041	GCA_002607735.1	1973495	1973495	type	True	78.0617	291	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:31,509] [INFO] DFAST Taxonomy check result was written to GCF_019048105.1_ASM1904810v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:31,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:31,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:31,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference/checkm_data
[2024-01-24 11:27:31,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:31,554] [INFO] Task started: CheckM
[2024-01-24 11:27:31,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048105.1_ASM1904810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048105.1_ASM1904810v1_genomic.fna/checkm_input GCF_019048105.1_ASM1904810v1_genomic.fna/checkm_result
[2024-01-24 11:28:06,400] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:06,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:06,422] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:06,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:06,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048105.1_ASM1904810v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:06,423] [INFO] Task started: Blastn
[2024-01-24 11:28:06,423] [INFO] Running command: blastn -query GCF_019048105.1_ASM1904810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga13db7de-f9c6-4d97-a81d-dd3392b27112/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048105.1_ASM1904810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:07,316] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:07,319] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:07,320] [INFO] Target genome list was writen to GCF_019048105.1_ASM1904810v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:07,333] [INFO] Task started: fastANI
[2024-01-24 11:28:07,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4eceed2-795f-4203-80b8-944f2cf44d46/GCF_019048105.1_ASM1904810v1_genomic.fna.gz --refList GCF_019048105.1_ASM1904810v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048105.1_ASM1904810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:17,786] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:17,804] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:17,805] [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
GCA_900455085.1	s__Providencia rettgeri	99.9752	1543	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.33	96.16	0.90	0.86	26	conclusive
GCF_013255915.1	s__Providencia rettgeri_D	92.1189	1258	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.61	97.24	0.90	0.84	55	-
GCF_002843235.3	s__Providencia huaxiensis	91.4058	1229	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.91	98.69	0.89	0.86	11	-
GCF_003936755.2	s__Providencia rettgeri_E	90.5785	1179	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874625.1	s__Providencia rettgeri_A	84.3705	1068	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	98.88	0.92	0.87	38	-
GCF_017151615.1	s__Providencia stuartii_C	83.564	1017	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_001655055.1	s__Providencia heimbachae	81.2423	849	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.30	99.03	0.95	0.93	6	-
GCF_000156395.1	s__Providencia rustigianii	81.1916	693	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.28	98.46	0.94	0.90	9	-
GCF_011045835.1	s__Proteus cibarius	78.7647	299	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.79	96.76	0.92	0.88	25	-
GCF_003144325.1	s__Proteus terrae	78.1288	286	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.30	96.81	0.93	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:17,807] [INFO] GTDB search result was written to GCF_019048105.1_ASM1904810v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:17,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:17,811] [INFO] DFAST_QC result json was written to GCF_019048105.1_ASM1904810v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:17,811] [INFO] DFAST_QC completed!
[2024-01-24 11:28:17,811] [INFO] Total running time: 0h1m13s