[2024-01-24 10:57:26,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,479] [INFO] DQC Reference Directory: /var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference
[2024-01-24 10:57:27,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,856] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg48f18b1f-c556-4398-98b0-27215444465a/GCF_019797845.1_ASM1979784v1_genomic.fna.gz | prodigal -d GCF_019797845.1_ASM1979784v1_genomic.fna/cds.fna -a GCF_019797845.1_ASM1979784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:42,096] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:42,096] [INFO] Task started: HMMsearch
[2024-01-24 10:57:42,096] [INFO] Running command: hmmsearch --tblout GCF_019797845.1_ASM1979784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference/reference_markers.hmm GCF_019797845.1_ASM1979784v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:42,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:42,403] [INFO] Found 6/6 markers.
[2024-01-24 10:57:42,442] [INFO] Query marker FASTA was written to GCF_019797845.1_ASM1979784v1_genomic.fna/markers.fasta
[2024-01-24 10:57:42,443] [INFO] Task started: Blastn
[2024-01-24 10:57:42,443] [INFO] Running command: blastn -query GCF_019797845.1_ASM1979784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference/reference_markers.fasta -out GCF_019797845.1_ASM1979784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:43,286] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:43,292] [INFO] Selected 33 target genomes.
[2024-01-24 10:57:43,293] [INFO] Target genome list was writen to GCF_019797845.1_ASM1979784v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:43,304] [INFO] Task started: fastANI
[2024-01-24 10:57:43,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f18b1f-c556-4398-98b0-27215444465a/GCF_019797845.1_ASM1979784v1_genomic.fna.gz --refList GCF_019797845.1_ASM1979784v1_genomic.fna/target_genomes.txt --output GCF_019797845.1_ASM1979784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:12,866] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:12,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:12,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:12,892] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:12,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:12,893] [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
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	79.5577	557	1647	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.422	544	1647	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	79.4216	538	1647	95	below_threshold
Pectobacterium actinidiae	strain=KKH3	GCA_000803315.1	1507808	1507808	type	True	79.3338	561	1647	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	79.2828	546	1647	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	79.2787	554	1647	95	below_threshold
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	79.2618	557	1647	95	below_threshold
Pectobacterium fontis	strain=M022	GCA_000803215.1	2558042	2558042	type	True	79.2473	503	1647	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	79.2024	525	1647	95	below_threshold
Pectobacterium betavasculorum	strain=NCPPB 2795	GCA_000749845.1	55207	55207	type	True	79.1998	508	1647	95	below_threshold
Pectobacterium punjabense	strain=SS95	GCA_003028395.1	2108399	2108399	type	True	79.1783	500	1647	95	below_threshold
Pectobacterium atrosepticum	strain=NCPPB 549	GCA_000749905.1	29471	29471	type	True	79.1395	533	1647	95	below_threshold
Pectobacterium zantedeschiae	strain=9M	GCA_004137795.1	2034769	2034769	type	True	79.1146	520	1647	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	79.0752	524	1647	95	below_threshold
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	79.0538	541	1647	95	below_threshold
Dickeya undicola	strain=2B12	GCA_000784735.1	1577887	1577887	type	True	79.0168	458	1647	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	79.0099	402	1647	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.9484	402	1647	95	below_threshold
Dickeya zeae	strain=NCPPB 2538	GCA_000406165.1	204042	204042	type	True	78.945	464	1647	95	below_threshold
Serratia rubidaea	strain=FDAARGOS_926	GCA_016026735.1	61652	61652	type	True	78.9188	407	1647	95	below_threshold
Lonsdalea britannica	strain=LMG 26267	GCA_002111595.1	1082704	1082704	type	True	78.7821	360	1647	95	below_threshold
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	78.7281	302	1647	95	below_threshold
Serratia rubidaea	strain=NBRC 103169	GCA_001598675.1	61652	61652	type	True	78.6387	397	1647	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	78.6022	313	1647	95	below_threshold
Lonsdalea iberica	strain=LMG 26264	GCA_002111585.1	1082703	1082703	type	True	78.5883	341	1647	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.5243	383	1647	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.5016	412	1647	95	below_threshold
Kluyvera intermedia	strain=NCTC12125	GCA_900635475.1	61648	61648	suspected-type	True	78.4148	315	1647	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	78.3941	379	1647	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.2724	329	1647	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.2596	296	1647	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	78.2211	293	1647	95	below_threshold
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	77.8515	297	1647	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,895] [INFO] DFAST Taxonomy check result was written to GCF_019797845.1_ASM1979784v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:12,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:12,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:12,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference/checkm_data
[2024-01-24 10:58:12,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:12,943] [INFO] Task started: CheckM
[2024-01-24 10:58:12,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019797845.1_ASM1979784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019797845.1_ASM1979784v1_genomic.fna/checkm_input GCF_019797845.1_ASM1979784v1_genomic.fna/checkm_result
[2024-01-24 10:58:56,747] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:56,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:56,769] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:56,769] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:56,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019797845.1_ASM1979784v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:56,770] [INFO] Task started: Blastn
[2024-01-24 10:58:56,770] [INFO] Running command: blastn -query GCF_019797845.1_ASM1979784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77b3cc4-73a7-491d-bd4d-ecca01508c8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019797845.1_ASM1979784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:57,825] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:57,829] [INFO] Selected 21 target genomes.
[2024-01-24 10:58:57,829] [INFO] Target genome list was writen to GCF_019797845.1_ASM1979784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:57,843] [INFO] Task started: fastANI
[2024-01-24 10:58:57,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f18b1f-c556-4398-98b0-27215444465a/GCF_019797845.1_ASM1979784v1_genomic.fna.gz --refList GCF_019797845.1_ASM1979784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019797845.1_ASM1979784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:18,068] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:18,084] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:59:18,084] [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_015762685.1	s__Symbiopectobacterium sp015762685	92.4855	1276	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Symbiopectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018777385.1	s__Symbiopectobacterium endolongispinus	92.0499	1261	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Symbiopectobacterium	95.0	98.06	96.15	0.91	0.84	3	-
GCF_015548865.1	s__Symbiopectobacterium marcescens_A	86.8106	1256	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Symbiopectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002307355.1	s__Pectobacterium polaris	79.4961	560	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_000803315.1	s__Pectobacterium actinidiae	79.3079	563	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_001742185.1	s__Pectobacterium wasabiae	79.3066	551	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	-
GCF_000754695.1	s__Pectobacterium brasiliense	79.2958	551	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_000803215.1	s__Pectobacterium fontis	79.2382	504	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000749845.1	s__Pectobacterium betavasculorum	79.1767	510	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	79.0082	402	1647	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	78.9398	399	1647	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_000982825.1	s__Cronobacter sakazakii	78.8706	333	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCA_000010085.1	s__Sodalis glossinidius	78.8409	224	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis	95.0	99.91	99.91	0.97	0.97	2	-
GCF_002111595.1	s__Lonsdalea britannica	78.7754	359	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.31	98.65	0.97	0.93	3	-
GCF_001277175.1	s__Cronobacter universalis	78.6375	331	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCF_008710095.1	s__Affinibrenneria salicis	78.6284	448	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Affinibrenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002111585.1	s__Lonsdalea iberica	78.5762	342	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	98.99	98.99	0.92	0.92	2	-
GCF_900635475.1	s__Kluyvera intermedia	78.4723	316	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.24	98.87	0.94	0.90	4	-
GCF_018323885.1	s__Citrobacter_A amalonaticus	78.4529	341	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.67	95.02	0.91	0.83	59	-
GCF_001266615.1	s__Kluyvera cryocrescens_A	78.0499	293	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001756855.1	s__Erwinia dacicola	78.0014	170	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:18,086] [INFO] GTDB search result was written to GCF_019797845.1_ASM1979784v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:18,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:18,092] [INFO] DFAST_QC result json was written to GCF_019797845.1_ASM1979784v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:18,092] [INFO] DFAST_QC completed!
[2024-01-24 10:59:18,092] [INFO] Total running time: 0h1m52s