[2023-06-29 12:22:35,065] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:22:35,068] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:22:35,068] [INFO] DQC Reference Directory: /var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference
[2023-06-29 12:22:36,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:22:36,330] [INFO] Task started: Prodigal
[2023-06-29 12:22:36,331] [INFO] Running command: gunzip -c /var/lib/cwl/stge3db0147-faba-4ca5-95d8-1ce7d4416b14/GCA_011754095.1_ASM1175409v1_genomic.fna.gz | prodigal -d GCA_011754095.1_ASM1175409v1_genomic.fna/cds.fna -a GCA_011754095.1_ASM1175409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:22:40,265] [INFO] Task succeeded: Prodigal
[2023-06-29 12:22:40,266] [INFO] Task started: HMMsearch
[2023-06-29 12:22:40,266] [INFO] Running command: hmmsearch --tblout GCA_011754095.1_ASM1175409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference/reference_markers.hmm GCA_011754095.1_ASM1175409v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:22:40,473] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:22:40,475] [INFO] Found 6/6 markers.
[2023-06-29 12:22:40,500] [INFO] Query marker FASTA was written to GCA_011754095.1_ASM1175409v1_genomic.fna/markers.fasta
[2023-06-29 12:22:40,500] [INFO] Task started: Blastn
[2023-06-29 12:22:40,501] [INFO] Running command: blastn -query GCA_011754095.1_ASM1175409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference/reference_markers.fasta -out GCA_011754095.1_ASM1175409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:41,234] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:41,239] [INFO] Selected 14 target genomes.
[2023-06-29 12:22:41,239] [INFO] Target genome list was writen to GCA_011754095.1_ASM1175409v1_genomic.fna/target_genomes.txt
[2023-06-29 12:22:41,242] [INFO] Task started: fastANI
[2023-06-29 12:22:41,242] [INFO] Running command: fastANI --query /var/lib/cwl/stge3db0147-faba-4ca5-95d8-1ce7d4416b14/GCA_011754095.1_ASM1175409v1_genomic.fna.gz --refList GCA_011754095.1_ASM1175409v1_genomic.fna/target_genomes.txt --output GCA_011754095.1_ASM1175409v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:22:51,908] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:51,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:22:51,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:22:51,925] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:22:51,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:22:51,926] [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
Serratia symbiotica	strain=CWBI-2.3	GCA_000821185.2	138074	138074	suspected-type	True	94.852	440	460	95	below_threshold
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	82.0361	389	460	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	81.9893	382	460	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	81.9717	387	460	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	81.1014	352	460	95	below_threshold
Serratia surfactantfaciens	strain=YD25	GCA_001642805.2	2741499	2741499	type	True	81.0642	351	460	95	below_threshold
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	80.9494	361	460	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	80.8925	337	460	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	80.8075	347	460	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	80.7935	348	460	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	80.7509	347	460	95	below_threshold
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	80.4853	354	460	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	77.7741	156	460	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	77.6029	157	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:22:51,928] [INFO] DFAST Taxonomy check result was written to GCA_011754095.1_ASM1175409v1_genomic.fna/tc_result.tsv
[2023-06-29 12:22:51,929] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:22:51,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:22:51,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference/checkm_data
[2023-06-29 12:22:51,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:22:51,949] [INFO] Task started: CheckM
[2023-06-29 12:22:51,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011754095.1_ASM1175409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011754095.1_ASM1175409v1_genomic.fna/checkm_input GCA_011754095.1_ASM1175409v1_genomic.fna/checkm_result
[2023-06-29 12:23:11,188] [INFO] Task succeeded: CheckM
[2023-06-29 12:23:11,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:23:11,210] [INFO] ===== Completeness check finished =====
[2023-06-29 12:23:11,210] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:23:11,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011754095.1_ASM1175409v1_genomic.fna/markers.fasta)
[2023-06-29 12:23:11,211] [INFO] Task started: Blastn
[2023-06-29 12:23:11,211] [INFO] Running command: blastn -query GCA_011754095.1_ASM1175409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9f9c11b-d92b-49b4-8264-aab64ca54b02/dqc_reference/reference_markers_gtdb.fasta -out GCA_011754095.1_ASM1175409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:23:12,219] [INFO] Task succeeded: Blastn
[2023-06-29 12:23:12,227] [INFO] Selected 11 target genomes.
[2023-06-29 12:23:12,228] [INFO] Target genome list was writen to GCA_011754095.1_ASM1175409v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:23:12,264] [INFO] Task started: fastANI
[2023-06-29 12:23:12,265] [INFO] Running command: fastANI --query /var/lib/cwl/stge3db0147-faba-4ca5-95d8-1ce7d4416b14/GCA_011754095.1_ASM1175409v1_genomic.fna.gz --refList GCA_011754095.1_ASM1175409v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011754095.1_ASM1175409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:23:20,143] [INFO] Task succeeded: fastANI
[2023-06-29 12:23:20,155] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:23:20,156] [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_011754095.1	s__Serratia symbiotica_D	100.0	455	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000821185.2	s__Serratia symbiotica	94.852	440	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.16	96.03	0.89	0.83	10	-
GCA_011754105.1	s__Serratia symbiotica_E	91.3155	390	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187015.1	s__Serratia ficaria	82.0302	389	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_001642805.2	s__Serratia surfactantfaciens	81.0642	351	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_016742975.1	s__Serratia nevei	81.0634	316	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_002220655.1	s__Serratia marcescens_K	80.9677	363	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_001902635.1	s__Serratia marcescens_F	80.9384	353	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591175.1	s__Serratia inhibens	80.8547	339	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	-
GCF_001590925.1	s__Serratia plymuthica	80.7509	347	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_900380265.1	s__Serratia_H symbiotica_A	78.9841	193	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_H	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:23:20,158] [INFO] GTDB search result was written to GCA_011754095.1_ASM1175409v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:23:20,158] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:23:20,162] [INFO] DFAST_QC result json was written to GCA_011754095.1_ASM1175409v1_genomic.fna/dqc_result.json
[2023-06-29 12:23:20,162] [INFO] DFAST_QC completed!
[2023-06-29 12:23:20,162] [INFO] Total running time: 0h0m45s