[2024-01-24 11:58:54,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:54,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:54,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference
[2024-01-24 11:58:57,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,422] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,422] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbb4069a-9927-4d99-8dab-6d803ef64411/GCF_900475855.1_46338_B02_genomic.fna.gz | prodigal -d GCF_900475855.1_46338_B02_genomic.fna/cds.fna -a GCF_900475855.1_46338_B02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:06,631] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:06,632] [INFO] Task started: HMMsearch
[2024-01-24 11:59:06,632] [INFO] Running command: hmmsearch --tblout GCF_900475855.1_46338_B02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference/reference_markers.hmm GCF_900475855.1_46338_B02_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:06,911] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:06,913] [INFO] Found 6/6 markers.
[2024-01-24 11:59:06,952] [INFO] Query marker FASTA was written to GCF_900475855.1_46338_B02_genomic.fna/markers.fasta
[2024-01-24 11:59:06,953] [INFO] Task started: Blastn
[2024-01-24 11:59:06,953] [INFO] Running command: blastn -query GCF_900475855.1_46338_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference/reference_markers.fasta -out GCF_900475855.1_46338_B02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:07,750] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:07,754] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:07,755] [INFO] Target genome list was writen to GCF_900475855.1_46338_B02_genomic.fna/target_genomes.txt
[2024-01-24 11:59:07,790] [INFO] Task started: fastANI
[2024-01-24 11:59:07,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb4069a-9927-4d99-8dab-6d803ef64411/GCF_900475855.1_46338_B02_genomic.fna.gz --refList GCF_900475855.1_46338_B02_genomic.fna/target_genomes.txt --output GCF_900475855.1_46338_B02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:20,386] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:20,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:20,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:20,412] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:20,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:20,412] [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 heimbachae	strain=NCTC12003	GCA_900475855.1	333962	333962	type	True	100.0	1427	1428	95	conclusive
Providencia heimbachae	strain=ATCC 35613	GCA_001655055.1	333962	333962	type	True	99.9356	1373	1428	95	conclusive
Providencia vermicola	strain=DSM 17385	GCA_020381325.1	333965	333965	suspected-type	True	81.3922	806	1428	95	below_threshold
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	81.3537	863	1428	95	below_threshold
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	81.3062	884	1428	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	80.88	753	1428	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	80.6973	749	1428	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	80.6733	685	1428	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	80.3066	680	1428	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	80.3063	660	1428	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.2342	52	1428	95	below_threshold
Providencia sneebia	strain=DSM 19967	GCA_000314895.2	516075	516075	type	True	79.9125	540	1428	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.7942	63	1428	95	below_threshold
Arsenophonus apicola	strain=ArsBeeUS	GCA_020268605.1	2879119	2879119	type	True	78.7569	125	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:20,413] [INFO] DFAST Taxonomy check result was written to GCF_900475855.1_46338_B02_genomic.fna/tc_result.tsv
[2024-01-24 11:59:20,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:20,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:20,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference/checkm_data
[2024-01-24 11:59:20,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:20,468] [INFO] Task started: CheckM
[2024-01-24 11:59:20,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475855.1_46338_B02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475855.1_46338_B02_genomic.fna/checkm_input GCF_900475855.1_46338_B02_genomic.fna/checkm_result
[2024-01-24 11:59:52,749] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:52,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:52,775] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:52,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:52,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475855.1_46338_B02_genomic.fna/markers.fasta)
[2024-01-24 11:59:52,776] [INFO] Task started: Blastn
[2024-01-24 11:59:52,777] [INFO] Running command: blastn -query GCF_900475855.1_46338_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c9b19b-efac-4faf-97cf-45a629fd6d75/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475855.1_46338_B02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:53,962] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:53,972] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:53,973] [INFO] Target genome list was writen to GCF_900475855.1_46338_B02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:53,987] [INFO] Task started: fastANI
[2024-01-24 11:59:53,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb4069a-9927-4d99-8dab-6d803ef64411/GCF_900475855.1_46338_B02_genomic.fna.gz --refList GCF_900475855.1_46338_B02_genomic.fna/target_genomes_gtdb.txt --output GCF_900475855.1_46338_B02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:05,287] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:05,312] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:05,313] [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_001655055.1	s__Providencia heimbachae	99.9356	1373	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.30	99.03	0.95	0.93	6	conclusive
GCA_003533305.1	s__Providencia sp003533305	82.2203	971	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.80	99.80	0.94	0.94	2	-
GCF_001874625.1	s__Providencia rettgeri_A	81.5731	819	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	98.88	0.92	0.87	38	-
GCF_013255915.1	s__Providencia rettgeri_D	81.3975	878	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.61	97.24	0.90	0.84	55	-
GCA_900455085.1	s__Providencia rettgeri	81.3919	854	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.33	96.16	0.90	0.86	26	-
GCF_017151615.1	s__Providencia stuartii_C	81.3447	843	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_002843235.3	s__Providencia huaxiensis	81.3079	881	1428	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	81.2937	853	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013702265.1	s__Providencia rettgeri_F	80.9161	754	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	97.64	96.33	0.91	0.89	3	-
GCF_000527275.1	s__Providencia alcalifaciens_A	80.8301	690	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.68	97.24	0.94	0.89	15	-
GCF_000156395.1	s__Providencia rustigianii	80.7106	747	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.28	98.46	0.94	0.90	9	-
GCF_000314855.2	s__Providencia burhodogranariea	80.2893	661	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,315] [INFO] GTDB search result was written to GCF_900475855.1_46338_B02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:05,316] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:05,324] [INFO] DFAST_QC result json was written to GCF_900475855.1_46338_B02_genomic.fna/dqc_result.json
[2024-01-24 12:00:05,324] [INFO] DFAST_QC completed!
[2024-01-24 12:00:05,324] [INFO] Total running time: 0h1m11s