[2024-01-24 12:21:53,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:53,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:53,625] [INFO] DQC Reference Directory: /var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference
[2024-01-24 12:21:54,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:54,854] [INFO] Task started: Prodigal
[2024-01-24 12:21:54,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg06ddb370-cf20-4e0d-b1bc-a8a73b9079d3/GCF_000314895.2_ASM31489v2_genomic.fna.gz | prodigal -d GCF_000314895.2_ASM31489v2_genomic.fna/cds.fna -a GCF_000314895.2_ASM31489v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:02,563] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:02,564] [INFO] Task started: HMMsearch
[2024-01-24 12:22:02,564] [INFO] Running command: hmmsearch --tblout GCF_000314895.2_ASM31489v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference/reference_markers.hmm GCF_000314895.2_ASM31489v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:02,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:02,877] [INFO] Found 6/6 markers.
[2024-01-24 12:22:02,909] [INFO] Query marker FASTA was written to GCF_000314895.2_ASM31489v2_genomic.fna/markers.fasta
[2024-01-24 12:22:02,910] [INFO] Task started: Blastn
[2024-01-24 12:22:02,910] [INFO] Running command: blastn -query GCF_000314895.2_ASM31489v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference/reference_markers.fasta -out GCF_000314895.2_ASM31489v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:03,648] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:03,651] [INFO] Selected 13 target genomes.
[2024-01-24 12:22:03,652] [INFO] Target genome list was writen to GCF_000314895.2_ASM31489v2_genomic.fna/target_genomes.txt
[2024-01-24 12:22:03,659] [INFO] Task started: fastANI
[2024-01-24 12:22:03,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ddb370-cf20-4e0d-b1bc-a8a73b9079d3/GCF_000314895.2_ASM31489v2_genomic.fna.gz --refList GCF_000314895.2_ASM31489v2_genomic.fna/target_genomes.txt --output GCF_000314895.2_ASM31489v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:14,347] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:14,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:14,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:14,360] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:14,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:14,360] [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 sneebia	strain=DSM 19967	GCA_000314895.2	516075	516075	type	True	99.9811	1184	1297	95	conclusive
Providencia thailandensis	strain=KCTC 23281	GCA_014652175.1	990144	990144	type	True	80.9152	650	1297	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	80.8656	652	1297	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	80.8424	640	1297	95	below_threshold
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	80.4251	535	1297	95	below_threshold
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	80.1457	550	1297	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	79.9497	493	1297	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	79.9183	496	1297	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	79.6991	458	1297	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.0799	174	1297	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	77.9735	154	1297	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	77.7113	175	1297	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	77.5507	177	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:14,367] [INFO] DFAST Taxonomy check result was written to GCF_000314895.2_ASM31489v2_genomic.fna/tc_result.tsv
[2024-01-24 12:22:14,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:14,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:14,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference/checkm_data
[2024-01-24 12:22:14,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:14,430] [INFO] Task started: CheckM
[2024-01-24 12:22:14,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000314895.2_ASM31489v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000314895.2_ASM31489v2_genomic.fna/checkm_input GCF_000314895.2_ASM31489v2_genomic.fna/checkm_result
[2024-01-24 12:22:42,970] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:42,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,989] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:42,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:42,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000314895.2_ASM31489v2_genomic.fna/markers.fasta)
[2024-01-24 12:22:42,990] [INFO] Task started: Blastn
[2024-01-24 12:22:42,990] [INFO] Running command: blastn -query GCF_000314895.2_ASM31489v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge436e830-9d1b-4abc-ac65-5d24e6dd881a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000314895.2_ASM31489v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:43,894] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:43,904] [INFO] Selected 18 target genomes.
[2024-01-24 12:22:43,904] [INFO] Target genome list was writen to GCF_000314895.2_ASM31489v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:43,916] [INFO] Task started: fastANI
[2024-01-24 12:22:43,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ddb370-cf20-4e0d-b1bc-a8a73b9079d3/GCF_000314895.2_ASM31489v2_genomic.fna.gz --refList GCF_000314895.2_ASM31489v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000314895.2_ASM31489v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:59,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:59,282] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:59,283] [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_000314895.2	s__Providencia sneebia	99.9811	1184	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000314855.2	s__Providencia burhodogranariea	80.8764	635	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016618195.1	s__Providencia stuartii_A	80.8644	652	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.56	98.52	0.92	0.91	4	-
GCA_900455155.1	s__Providencia stuartii	80.8615	648	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	99.04	0.93	0.88	53	-
GCF_010748935.1	s__Providencia vermicola_A	80.769	646	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.27	99.19	0.95	0.94	4	-
GCA_900455085.1	s__Providencia rettgeri	80.3759	531	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.33	96.16	0.90	0.86	26	-
GCF_013255915.1	s__Providencia rettgeri_D	80.2823	543	1297	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	80.1458	548	1297	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	80.1456	527	1297	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	80.0956	551	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	98.88	0.92	0.87	38	-
GCF_000156395.1	s__Providencia rustigianii	79.959	492	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.28	98.46	0.94	0.90	9	-
GCF_017151615.1	s__Providencia stuartii_C	79.8463	543	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_013702265.1	s__Providencia rettgeri_F	79.8081	496	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	97.64	96.33	0.91	0.89	3	-
GCF_000173415.1	s__Providencia alcalifaciens	79.6709	461	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.05	98.75	0.92	0.89	24	-
GCF_000527275.1	s__Providencia alcalifaciens_A	79.5929	479	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.68	97.24	0.94	0.89	15	-
GCA_003533305.1	s__Providencia sp003533305	79.5165	569	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.80	99.80	0.94	0.94	2	-
GCF_005843885.1	s__Escherichia sp005843885	78.3069	83	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_004211955.1	s__Escherichia sp004211955	77.4762	75	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:59,285] [INFO] GTDB search result was written to GCF_000314895.2_ASM31489v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:59,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:59,291] [INFO] DFAST_QC result json was written to GCF_000314895.2_ASM31489v2_genomic.fna/dqc_result.json
[2024-01-24 12:22:59,291] [INFO] DFAST_QC completed!
[2024-01-24 12:22:59,291] [INFO] Total running time: 0h1m6s