[2024-01-24 15:10:23,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,254] [INFO] DQC Reference Directory: /var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference
[2024-01-24 15:10:24,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,738] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg30217fe8-3d95-49f3-8097-14e395fb6cb1/GCF_014652175.1_ASM1465217v1_genomic.fna.gz | prodigal -d GCF_014652175.1_ASM1465217v1_genomic.fna/cds.fna -a GCF_014652175.1_ASM1465217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:34,625] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:34,626] [INFO] Task started: HMMsearch
[2024-01-24 15:10:34,626] [INFO] Running command: hmmsearch --tblout GCF_014652175.1_ASM1465217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference/reference_markers.hmm GCF_014652175.1_ASM1465217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:34,938] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:34,939] [INFO] Found 6/6 markers.
[2024-01-24 15:10:34,976] [INFO] Query marker FASTA was written to GCF_014652175.1_ASM1465217v1_genomic.fna/markers.fasta
[2024-01-24 15:10:34,976] [INFO] Task started: Blastn
[2024-01-24 15:10:34,976] [INFO] Running command: blastn -query GCF_014652175.1_ASM1465217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference/reference_markers.fasta -out GCF_014652175.1_ASM1465217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:35,718] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:35,721] [INFO] Selected 14 target genomes.
[2024-01-24 15:10:35,722] [INFO] Target genome list was writen to GCF_014652175.1_ASM1465217v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:35,727] [INFO] Task started: fastANI
[2024-01-24 15:10:35,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg30217fe8-3d95-49f3-8097-14e395fb6cb1/GCF_014652175.1_ASM1465217v1_genomic.fna.gz --refList GCF_014652175.1_ASM1465217v1_genomic.fna/target_genomes.txt --output GCF_014652175.1_ASM1465217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:48,472] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:48,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:48,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:48,485] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:48,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:48,485] [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 thailandensis	strain=KCTC 23281	GCA_014652175.1	990144	990144	type	True	100.0	1431	1431	95	conclusive
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	82.5364	938	1431	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	81.9686	811	1431	95	below_threshold
Providencia sneebia	strain=DSM 19967	GCA_000314895.2	516075	516075	type	True	80.9137	632	1431	95	below_threshold
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	80.5378	654	1431	95	below_threshold
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	80.2934	637	1431	95	below_threshold
Providencia heimbachae	strain=NCTC12003	GCA_900475855.1	333962	333962	type	True	80.15	648	1431	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	80.0562	567	1431	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	80.0398	576	1431	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	79.7162	582	1431	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	78.4753	182	1431	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.1782	182	1431	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.133	184	1431	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	77.9936	188	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:48,490] [INFO] DFAST Taxonomy check result was written to GCF_014652175.1_ASM1465217v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:48,491] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:48,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:48,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference/checkm_data
[2024-01-24 15:10:48,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:48,537] [INFO] Task started: CheckM
[2024-01-24 15:10:48,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652175.1_ASM1465217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652175.1_ASM1465217v1_genomic.fna/checkm_input GCF_014652175.1_ASM1465217v1_genomic.fna/checkm_result
[2024-01-24 15:11:22,664] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:22,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:22,685] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:22,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:22,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652175.1_ASM1465217v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:22,686] [INFO] Task started: Blastn
[2024-01-24 15:11:22,686] [INFO] Running command: blastn -query GCF_014652175.1_ASM1465217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783fe873-93a0-4cbe-9f9b-672f2b48a07e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652175.1_ASM1465217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:23,726] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:23,730] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:23,730] [INFO] Target genome list was writen to GCF_014652175.1_ASM1465217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:23,739] [INFO] Task started: fastANI
[2024-01-24 15:11:23,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg30217fe8-3d95-49f3-8097-14e395fb6cb1/GCF_014652175.1_ASM1465217v1_genomic.fna.gz --refList GCF_014652175.1_ASM1465217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652175.1_ASM1465217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:36,418] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:36,429] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:36,430] [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_900455155.1	s__Providencia stuartii	99.1282	1329	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	99.04	0.93	0.88	53	conclusive
GCF_010748935.1	s__Providencia vermicola_A	84.2963	1041	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.27	99.19	0.95	0.94	4	-
GCA_016618195.1	s__Providencia stuartii_A	82.5318	939	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.56	98.52	0.92	0.91	4	-
GCF_000314855.2	s__Providencia burhodogranariea	81.951	813	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314895.2	s__Providencia sneebia	80.9171	633	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013255915.1	s__Providencia rettgeri_D	80.4828	659	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.61	97.24	0.90	0.84	55	-
GCF_003936755.2	s__Providencia rettgeri_E	80.3603	643	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843235.3	s__Providencia huaxiensis	80.3023	636	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.91	98.69	0.89	0.86	11	-
GCF_013702265.1	s__Providencia rettgeri_F	80.2593	577	1431	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	79.9717	575	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.68	97.24	0.94	0.89	15	-
GCF_000173415.1	s__Providencia alcalifaciens	79.7162	582	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.05	98.75	0.92	0.89	24	-
GCF_009914335.1	s__Proteus sp003144505	78.2668	265	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.18	97.72	0.94	0.91	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:36,431] [INFO] GTDB search result was written to GCF_014652175.1_ASM1465217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:36,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:36,436] [INFO] DFAST_QC result json was written to GCF_014652175.1_ASM1465217v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:36,436] [INFO] DFAST_QC completed!
[2024-01-24 15:11:36,436] [INFO] Total running time: 0h1m13s