[2024-01-24 14:28:17,877] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,879] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference
[2024-01-24 14:28:20,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,484] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg8721e03b-7afa-4e48-979b-48d42aecff17/GCF_900635445.1_28869_A02_genomic.fna.gz | prodigal -d GCF_900635445.1_28869_A02_genomic.fna/cds.fna -a GCF_900635445.1_28869_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:37,414] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:37,414] [INFO] Task started: HMMsearch
[2024-01-24 14:28:37,414] [INFO] Running command: hmmsearch --tblout GCF_900635445.1_28869_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference/reference_markers.hmm GCF_900635445.1_28869_A02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:37,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:37,746] [INFO] Found 6/6 markers.
[2024-01-24 14:28:37,796] [INFO] Query marker FASTA was written to GCF_900635445.1_28869_A02_genomic.fna/markers.fasta
[2024-01-24 14:28:37,796] [INFO] Task started: Blastn
[2024-01-24 14:28:37,796] [INFO] Running command: blastn -query GCF_900635445.1_28869_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference/reference_markers.fasta -out GCF_900635445.1_28869_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:38,766] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:38,780] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:38,781] [INFO] Target genome list was writen to GCF_900635445.1_28869_A02_genomic.fna/target_genomes.txt
[2024-01-24 14:28:38,788] [INFO] Task started: fastANI
[2024-01-24 14:28:38,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg8721e03b-7afa-4e48-979b-48d42aecff17/GCF_900635445.1_28869_A02_genomic.fna.gz --refList GCF_900635445.1_28869_A02_genomic.fna/target_genomes.txt --output GCF_900635445.1_28869_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:56,003] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:56,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:56,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:56,019] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:56,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:56,020] [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 odorifera	strain=NCTC11214	GCA_900635445.1	618	618	type	True	100.0	1757	1757	95	conclusive
Serratia odorifera	strain=DSM 4582	GCA_000163595.1	618	618	type	True	99.8461	1707	1757	95	conclusive
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	83.6645	1100	1757	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	83.6235	1115	1757	95	below_threshold
Serratia rubidaea	strain=FDAARGOS_926	GCA_016026735.1	61652	61652	type	True	83.6198	1109	1757	95	below_threshold
Serratia rubidaea	strain=NBRC 103169	GCA_001598675.1	61652	61652	type	True	83.5072	1086	1757	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	83.4318	1019	1757	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	83.4236	1104	1757	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	83.4026	1110	1757	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	83.3903	1110	1757	95	below_threshold
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	83.2395	1119	1757	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	83.2341	1098	1757	95	below_threshold
Serratia nematodiphila	strain=CGMCC 1.6853	GCA_900101535.1	458197	458197	suspected-type	True	83.2011	1081	1757	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	83.0981	1075	1757	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.0753	569	1757	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.0601	589	1757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:56,021] [INFO] DFAST Taxonomy check result was written to GCF_900635445.1_28869_A02_genomic.fna/tc_result.tsv
[2024-01-24 14:28:56,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:56,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:56,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference/checkm_data
[2024-01-24 14:28:56,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:56,078] [INFO] Task started: CheckM
[2024-01-24 14:28:56,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900635445.1_28869_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900635445.1_28869_A02_genomic.fna/checkm_input GCF_900635445.1_28869_A02_genomic.fna/checkm_result
[2024-01-24 14:29:44,353] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:44,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:44,376] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:44,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:44,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900635445.1_28869_A02_genomic.fna/markers.fasta)
[2024-01-24 14:29:44,377] [INFO] Task started: Blastn
[2024-01-24 14:29:44,377] [INFO] Running command: blastn -query GCF_900635445.1_28869_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg03398f86-7757-4fc9-9779-ca420a44ab27/dqc_reference/reference_markers_gtdb.fasta -out GCF_900635445.1_28869_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:45,858] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:45,863] [INFO] Selected 17 target genomes.
[2024-01-24 14:29:45,863] [INFO] Target genome list was writen to GCF_900635445.1_28869_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:45,866] [INFO] Task started: fastANI
[2024-01-24 14:29:45,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg8721e03b-7afa-4e48-979b-48d42aecff17/GCF_900635445.1_28869_A02_genomic.fna.gz --refList GCF_900635445.1_28869_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900635445.1_28869_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:05,380] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:05,398] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:05,399] [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_900635445.1	s__Serratia_F odorifera	100.0	1757	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_F	95.0	99.83	99.53	0.98	0.94	5	conclusive
GCF_900187015.1	s__Serratia ficaria	83.8356	1175	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	83.6224	1114	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
GCA_901472405.1	s__Serratia_B rubidaea	83.594	1116	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	98.79	97.55	0.96	0.91	11	-
GCF_017299535.1	s__Serratia marcescens	83.3932	1114	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_002220655.1	s__Serratia marcescens_K	83.3923	1128	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_001642805.2	s__Serratia surfactantfaciens	83.3805	1085	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_006715005.1	s__Serratia marcescens_J	83.3308	1104	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_001902635.1	s__Serratia marcescens_F	83.3221	1032	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016742975.1	s__Serratia nevei	83.2608	960	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_000738675.1	s__Serratia nematodiphila	83.2546	1120	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_900457075.1	s__Serratia quinivorans	82.7264	1109	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.38	95.64	0.93	0.85	9	-
GCF_017832355.1	s__Serratia sp017832355	81.9002	966	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006005.1	s__Serratia_A fonticola	81.8837	957	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	-
GCF_001976145.1	s__Chania oryzae	81.7551	846	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_000633355.1	s__Serratia_A sp000633355	81.7466	924	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002291425.1	s__Gibbsiella quercinecans	81.7008	885	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gibbsiella	95.0	99.45	98.17	0.96	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:05,400] [INFO] GTDB search result was written to GCF_900635445.1_28869_A02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:05,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:05,408] [INFO] DFAST_QC result json was written to GCF_900635445.1_28869_A02_genomic.fna/dqc_result.json
[2024-01-24 14:30:05,408] [INFO] DFAST_QC completed!
[2024-01-24 14:30:05,408] [INFO] Total running time: 0h1m48s