[2024-01-25 20:21:05,610] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:05,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:05,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference
[2024-01-25 20:21:06,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:06,815] [INFO] Task started: Prodigal
[2024-01-25 20:21:06,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d8acc15-7784-47f8-a044-4f439de8eca6/GCF_001006005.1_ASM100600v1_genomic.fna.gz | prodigal -d GCF_001006005.1_ASM100600v1_genomic.fna/cds.fna -a GCF_001006005.1_ASM100600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:26,197] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:26,197] [INFO] Task started: HMMsearch
[2024-01-25 20:21:26,197] [INFO] Running command: hmmsearch --tblout GCF_001006005.1_ASM100600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference/reference_markers.hmm GCF_001006005.1_ASM100600v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:26,466] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:26,467] [INFO] Found 6/6 markers.
[2024-01-25 20:21:26,513] [INFO] Query marker FASTA was written to GCF_001006005.1_ASM100600v1_genomic.fna/markers.fasta
[2024-01-25 20:21:26,514] [INFO] Task started: Blastn
[2024-01-25 20:21:26,514] [INFO] Running command: blastn -query GCF_001006005.1_ASM100600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference/reference_markers.fasta -out GCF_001006005.1_ASM100600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:27,328] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:27,331] [INFO] Selected 22 target genomes.
[2024-01-25 20:21:27,331] [INFO] Target genome list was writen to GCF_001006005.1_ASM100600v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:27,340] [INFO] Task started: fastANI
[2024-01-25 20:21:27,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d8acc15-7784-47f8-a044-4f439de8eca6/GCF_001006005.1_ASM100600v1_genomic.fna.gz --refList GCF_001006005.1_ASM100600v1_genomic.fna/target_genomes.txt --output GCF_001006005.1_ASM100600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:50,295] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:50,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:50,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:50,308] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:21:50,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:50,308] [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 fonticola	strain=DSM 4576	GCA_001006005.1	47917	47917	suspected-type	True	100.0	2000	2000	95	conclusive
Serratia fonticola	strain=LMG 7882	GCA_000469035.1	47917	47917	suspected-type	True	99.8655	1778	2000	95	conclusive
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	82.8717	1019	2000	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	82.7216	1026	2000	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	82.6057	988	2000	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	82.5973	1006	2000	95	below_threshold
Serratia liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	82.4653	1050	2000	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	82.4516	1026	2000	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	82.4469	1016	2000	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	82.4381	1017	2000	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	82.3296	1020	2000	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	82.2265	995	2000	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	81.8558	971	2000	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000520015.2	1639108	1639108	type	True	81.8188	1010	2000	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000568195.1	1639108	1639108	type	True	81.7103	990	2000	95	below_threshold
Serratia grimesii	strain=NBRC 13537	GCA_001590905.1	82995	82995	type	True	81.6568	960	2000	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	80.9138	795	2000	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.3259	537	2000	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.9209	518	2000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:50,310] [INFO] DFAST Taxonomy check result was written to GCF_001006005.1_ASM100600v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:50,310] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:50,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:50,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference/checkm_data
[2024-01-25 20:21:50,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:50,382] [INFO] Task started: CheckM
[2024-01-25 20:21:50,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001006005.1_ASM100600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001006005.1_ASM100600v1_genomic.fna/checkm_input GCF_001006005.1_ASM100600v1_genomic.fna/checkm_result
[2024-01-25 20:22:42,814] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:42,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:42,833] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:42,833] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:42,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001006005.1_ASM100600v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:42,834] [INFO] Task started: Blastn
[2024-01-25 20:22:42,834] [INFO] Running command: blastn -query GCF_001006005.1_ASM100600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa3f871c-e99d-450e-816d-8d4d8c7bbec0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001006005.1_ASM100600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:43,997] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:44,000] [INFO] Selected 16 target genomes.
[2024-01-25 20:22:44,000] [INFO] Target genome list was writen to GCF_001006005.1_ASM100600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:44,019] [INFO] Task started: fastANI
[2024-01-25 20:22:44,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d8acc15-7784-47f8-a044-4f439de8eca6/GCF_001006005.1_ASM100600v1_genomic.fna.gz --refList GCF_001006005.1_ASM100600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001006005.1_ASM100600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:02,942] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:02,951] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:02,951] [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_001006005.1	s__Serratia_A fonticola	100.0	2000	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	conclusive
GCF_000633355.1	s__Serratia_A sp000633355	90.1654	1519	2000	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_006715025.1	s__Serratia_A fonticola_A	84.9359	1329	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	4	-
GCF_001976145.1	s__Chania oryzae	83.3197	1053	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_900187015.1	s__Serratia ficaria	82.6313	1047	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_001590925.1	s__Serratia plymuthica	82.5968	988	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_003591175.1	s__Serratia inhibens	82.5894	1007	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	-
GCF_000743355.1	s__Chania sp000743355	82.4694	993	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_013337185.1	s__Serratia proteamaculans_D	82.4668	1025	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.78	95.57	0.96	0.91	3	-
GCF_016742975.1	s__Serratia nevei	82.4401	892	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_000422085.1	s__Serratia liquefaciens	82.432	1050	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.63	98.20	0.94	0.91	25	-
GCF_003812745.1	s__Serratia sp003812745	82.417	1002	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCA_012719855.1	s__Serratia liquefaciens_A	82.2694	1021	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
GCF_009831415.1	s__Yersinia canariae	79.796	462	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:02,952] [INFO] GTDB search result was written to GCF_001006005.1_ASM100600v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:02,953] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:02,956] [INFO] DFAST_QC result json was written to GCF_001006005.1_ASM100600v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:02,956] [INFO] DFAST_QC completed!
[2024-01-25 20:23:02,956] [INFO] Total running time: 0h1m57s