[2024-01-25 20:14:05,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:05,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:05,627] [INFO] DQC Reference Directory: /var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference
[2024-01-25 20:14:06,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:06,774] [INFO] Task started: Prodigal
[2024-01-25 20:14:06,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bc04a35-db6e-4580-ada3-d0f21f71f062/GCF_016026735.1_ASM1602673v1_genomic.fna.gz | prodigal -d GCF_016026735.1_ASM1602673v1_genomic.fna/cds.fna -a GCF_016026735.1_ASM1602673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:18,731] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:18,732] [INFO] Task started: HMMsearch
[2024-01-25 20:14:18,732] [INFO] Running command: hmmsearch --tblout GCF_016026735.1_ASM1602673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference/reference_markers.hmm GCF_016026735.1_ASM1602673v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:19,030] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:19,033] [INFO] Found 6/6 markers.
[2024-01-25 20:14:19,075] [INFO] Query marker FASTA was written to GCF_016026735.1_ASM1602673v1_genomic.fna/markers.fasta
[2024-01-25 20:14:19,075] [INFO] Task started: Blastn
[2024-01-25 20:14:19,075] [INFO] Running command: blastn -query GCF_016026735.1_ASM1602673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference/reference_markers.fasta -out GCF_016026735.1_ASM1602673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:19,973] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:19,976] [INFO] Selected 12 target genomes.
[2024-01-25 20:14:19,976] [INFO] Target genome list was writen to GCF_016026735.1_ASM1602673v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:19,983] [INFO] Task started: fastANI
[2024-01-25 20:14:19,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bc04a35-db6e-4580-ada3-d0f21f71f062/GCF_016026735.1_ASM1602673v1_genomic.fna.gz --refList GCF_016026735.1_ASM1602673v1_genomic.fna/target_genomes.txt --output GCF_016026735.1_ASM1602673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:34,083] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:34,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:34,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:34,092] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:14:34,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:34,092] [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 rubidaea	strain=FDAARGOS_926	GCA_016026735.1	61652	61652	type	True	100.0	1664	1665	95	conclusive
Serratia rubidaea	strain=NBRC 103169	GCA_001598675.1	61652	61652	type	True	99.9929	1635	1665	95	conclusive
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	99.8998	1481	1665	95	conclusive
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	92.8926	1451	1665	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	84.747	1132	1665	95	below_threshold
Serratia ureilytica	strain=CCUG:50595	GCA_013375155.1	300181	300181	type	True	84.6381	1108	1665	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	84.6294	1109	1665	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	84.3836	1078	1665	95	below_threshold
Serratia odorifera	strain=NCTC11214	GCA_900635445.1	618	618	type	True	83.6975	1096	1665	95	below_threshold
Serratia odorifera	strain=DSM 4582	GCA_000163595.1	618	618	type	True	83.5883	1090	1665	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.0926	615	1665	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.9675	565	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:34,094] [INFO] DFAST Taxonomy check result was written to GCF_016026735.1_ASM1602673v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:34,095] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:34,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:34,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference/checkm_data
[2024-01-25 20:14:34,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:34,143] [INFO] Task started: CheckM
[2024-01-25 20:14:34,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016026735.1_ASM1602673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016026735.1_ASM1602673v1_genomic.fna/checkm_input GCF_016026735.1_ASM1602673v1_genomic.fna/checkm_result
[2024-01-25 20:15:10,811] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:10,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:10,843] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:10,843] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:10,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016026735.1_ASM1602673v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:10,844] [INFO] Task started: Blastn
[2024-01-25 20:15:10,844] [INFO] Running command: blastn -query GCF_016026735.1_ASM1602673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e9f381-246a-498b-a259-7cff43838ab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016026735.1_ASM1602673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:12,107] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:12,109] [INFO] Selected 15 target genomes.
[2024-01-25 20:15:12,109] [INFO] Target genome list was writen to GCF_016026735.1_ASM1602673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:12,118] [INFO] Task started: fastANI
[2024-01-25 20:15:12,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bc04a35-db6e-4580-ada3-d0f21f71f062/GCF_016026735.1_ASM1602673v1_genomic.fna.gz --refList GCF_016026735.1_ASM1602673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016026735.1_ASM1602673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:28,201] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:28,209] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:28,210] [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_901472405.1	s__Serratia_B rubidaea	99.9137	1664	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	98.79	97.55	0.96	0.91	11	conclusive
GCF_009817885.1	s__Serratia_B rhizosphaerae	92.8922	1451	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
GCF_900187015.1	s__Serratia ficaria	84.9763	1212	1665	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	84.9045	1118	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_000738675.1	s__Serratia nematodiphila	84.8185	1134	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_017299535.1	s__Serratia marcescens	84.8128	1106	1665	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	84.7274	1110	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_013375155.1	s__Serratia ureilytica	84.6227	1110	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_003812745.1	s__Serratia sp003812745	84.5558	1100	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCF_001642805.2	s__Serratia surfactantfaciens	84.5402	1119	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_000513215.1	s__Serratia bockelmannii	84.4935	1103	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCF_001902635.1	s__Serratia marcescens_F	84.3728	1065	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635445.1	s__Serratia_F odorifera	83.6945	1095	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_F	95.0	99.83	99.53	0.98	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:28,211] [INFO] GTDB search result was written to GCF_016026735.1_ASM1602673v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:28,212] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:28,214] [INFO] DFAST_QC result json was written to GCF_016026735.1_ASM1602673v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:28,215] [INFO] DFAST_QC completed!
[2024-01-25 20:15:28,215] [INFO] Total running time: 0h1m23s