[2024-01-24 11:43:25,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference
[2024-01-24 11:43:30,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,056] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg706743fb-e530-4a75-8c7e-c4c6118e1f71/GCF_000821185.2_ASM82118v2_genomic.fna.gz | prodigal -d GCF_000821185.2_ASM82118v2_genomic.fna/cds.fna -a GCF_000821185.2_ASM82118v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:42,035] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:42,035] [INFO] Task started: HMMsearch
[2024-01-24 11:43:42,035] [INFO] Running command: hmmsearch --tblout GCF_000821185.2_ASM82118v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference/reference_markers.hmm GCF_000821185.2_ASM82118v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:42,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:42,305] [INFO] Found 6/6 markers.
[2024-01-24 11:43:42,336] [INFO] Query marker FASTA was written to GCF_000821185.2_ASM82118v2_genomic.fna/markers.fasta
[2024-01-24 11:43:42,336] [INFO] Task started: Blastn
[2024-01-24 11:43:42,337] [INFO] Running command: blastn -query GCF_000821185.2_ASM82118v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference/reference_markers.fasta -out GCF_000821185.2_ASM82118v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,139] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,143] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:43,143] [INFO] Target genome list was writen to GCF_000821185.2_ASM82118v2_genomic.fna/target_genomes.txt
[2024-01-24 11:43:43,149] [INFO] Task started: fastANI
[2024-01-24 11:43:43,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg706743fb-e530-4a75-8c7e-c4c6118e1f71/GCF_000821185.2_ASM82118v2_genomic.fna.gz --refList GCF_000821185.2_ASM82118v2_genomic.fna/target_genomes.txt --output GCF_000821185.2_ASM82118v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:56,051] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:56,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:56,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:56,066] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:56,067] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:56,067] [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	100.0	1176	1182	95	conclusive
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	83.3819	677	1182	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	83.3522	671	1182	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	83.1397	667	1182	95	below_threshold
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	82.2855	623	1182	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	82.1872	624	1182	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	82.155	617	1182	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	81.8493	600	1182	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	81.8432	595	1182	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	81.8393	590	1182	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	81.8226	623	1182	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.7599	267	1182	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.4462	308	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:56,068] [INFO] DFAST Taxonomy check result was written to GCF_000821185.2_ASM82118v2_genomic.fna/tc_result.tsv
[2024-01-24 11:43:56,069] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:56,069] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:56,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference/checkm_data
[2024-01-24 11:43:56,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:56,106] [INFO] Task started: CheckM
[2024-01-24 11:43:56,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000821185.2_ASM82118v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000821185.2_ASM82118v2_genomic.fna/checkm_input GCF_000821185.2_ASM82118v2_genomic.fna/checkm_result
[2024-01-24 11:44:34,579] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:34,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:34,596] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:34,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:34,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000821185.2_ASM82118v2_genomic.fna/markers.fasta)
[2024-01-24 11:44:34,597] [INFO] Task started: Blastn
[2024-01-24 11:44:34,597] [INFO] Running command: blastn -query GCF_000821185.2_ASM82118v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg193955ef-0d60-4b77-a5e8-9b6b9eef6692/dqc_reference/reference_markers_gtdb.fasta -out GCF_000821185.2_ASM82118v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,633] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,637] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:35,637] [INFO] Target genome list was writen to GCF_000821185.2_ASM82118v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:35,647] [INFO] Task started: fastANI
[2024-01-24 11:44:35,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg706743fb-e530-4a75-8c7e-c4c6118e1f71/GCF_000821185.2_ASM82118v2_genomic.fna.gz --refList GCF_000821185.2_ASM82118v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000821185.2_ASM82118v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:46,924] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:46,938] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:46,938] [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_000821185.2	s__Serratia symbiotica	100.0	1176	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.16	96.03	0.89	0.83	10	conclusive
GCA_011754095.1	s__Serratia symbiotica_D	94.631	445	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011754105.1	s__Serratia symbiotica_E	90.7154	459	1182	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	83.3742	675	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_002220655.1	s__Serratia marcescens_K	82.1947	621	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_017299535.1	s__Serratia marcescens	82.1852	622	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_006715005.1	s__Serratia marcescens_J	82.1612	636	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_001642805.2	s__Serratia surfactantfaciens	82.0847	618	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_013375155.1	s__Serratia ureilytica	81.8834	612	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_003591175.1	s__Serratia inhibens	81.8618	599	1182	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	81.846	595	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_000312485.1	s__Yersinia massiliensis	78.6902	246	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.58	95.54	0.91	0.88	22	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:46,940] [INFO] GTDB search result was written to GCF_000821185.2_ASM82118v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:46,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:46,944] [INFO] DFAST_QC result json was written to GCF_000821185.2_ASM82118v2_genomic.fna/dqc_result.json
[2024-01-24 11:44:46,944] [INFO] DFAST_QC completed!
[2024-01-24 11:44:46,944] [INFO] Total running time: 0h1m22s