[2024-01-24 15:02:36,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference
[2024-01-24 15:02:38,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,277] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc814265-e1c9-4cab-aff2-740c5bf015a4/GCF_008710095.1_ASM871009v1_genomic.fna.gz | prodigal -d GCF_008710095.1_ASM871009v1_genomic.fna/cds.fna -a GCF_008710095.1_ASM871009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:54,580] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:54,580] [INFO] Task started: HMMsearch
[2024-01-24 15:02:54,580] [INFO] Running command: hmmsearch --tblout GCF_008710095.1_ASM871009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference/reference_markers.hmm GCF_008710095.1_ASM871009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:54,926] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:54,927] [INFO] Found 6/6 markers.
[2024-01-24 15:02:54,980] [INFO] Query marker FASTA was written to GCF_008710095.1_ASM871009v1_genomic.fna/markers.fasta
[2024-01-24 15:02:54,980] [INFO] Task started: Blastn
[2024-01-24 15:02:54,981] [INFO] Running command: blastn -query GCF_008710095.1_ASM871009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference/reference_markers.fasta -out GCF_008710095.1_ASM871009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:55,968] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:55,976] [INFO] Selected 28 target genomes.
[2024-01-24 15:02:55,976] [INFO] Target genome list was writen to GCF_008710095.1_ASM871009v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:55,989] [INFO] Task started: fastANI
[2024-01-24 15:02:55,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc814265-e1c9-4cab-aff2-740c5bf015a4/GCF_008710095.1_ASM871009v1_genomic.fna.gz --refList GCF_008710095.1_ASM871009v1_genomic.fna/target_genomes.txt --output GCF_008710095.1_ASM871009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:23,785] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:23,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:23,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:23,807] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:23,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:23,807] [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
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	80.4584	738	1941	95	below_threshold
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	80.455	749	1941	95	below_threshold
Brenneria izadpanahii	strain=Iran 50	GCA_017569925.1	2722756	2722756	type	True	80.2418	705	1941	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_002291445.1	1109412	1109412	type	True	80.0885	694	1941	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_003666235.1	1109412	1109412	type	True	80.043	675	1941	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	79.9097	567	1941	95	below_threshold
Serratia rubidaea	strain=FDAARGOS_926	GCA_016026735.1	61652	61652	type	True	79.7215	644	1941	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	79.6957	625	1941	95	below_threshold
Serratia rubidaea	strain=NBRC 103169	GCA_001598675.1	61652	61652	type	True	79.6508	634	1941	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	79.6089	599	1941	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	79.6008	625	1941	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	79.533	552	1941	95	below_threshold
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	79.5315	671	1941	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	79.53	645	1941	95	below_threshold
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	79.5228	649	1941	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	79.5221	637	1941	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	79.5057	639	1941	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	79.4796	643	1941	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.4752	605	1941	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S37_jyu2015	GCA_017301315.1	615	615	suspected-type	True	79.4642	645	1941	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.4301	632	1941	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	79.4286	657	1941	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	79.3265	640	1941	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.3238	654	1941	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	79.1183	668	1941	95	below_threshold
Chimaeribacter coloradensis	strain=2016-Iso4	GCA_002858715.1	2060068	2060068	type	True	78.7574	498	1941	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	78.6909	495	1941	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.0282	389	1941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:23,821] [INFO] DFAST Taxonomy check result was written to GCF_008710095.1_ASM871009v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:23,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:23,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:23,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference/checkm_data
[2024-01-24 15:03:23,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:23,883] [INFO] Task started: CheckM
[2024-01-24 15:03:23,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008710095.1_ASM871009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008710095.1_ASM871009v1_genomic.fna/checkm_input GCF_008710095.1_ASM871009v1_genomic.fna/checkm_result
[2024-01-24 15:04:11,710] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:11,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 29.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:11,742] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:11,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:11,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008710095.1_ASM871009v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:11,743] [INFO] Task started: Blastn
[2024-01-24 15:04:11,743] [INFO] Running command: blastn -query GCF_008710095.1_ASM871009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba9118c2-04bf-4dc2-8f4a-143b979cd1c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008710095.1_ASM871009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:13,069] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:13,072] [INFO] Selected 18 target genomes.
[2024-01-24 15:04:13,073] [INFO] Target genome list was writen to GCF_008710095.1_ASM871009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:13,091] [INFO] Task started: fastANI
[2024-01-24 15:04:13,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc814265-e1c9-4cab-aff2-740c5bf015a4/GCF_008710095.1_ASM871009v1_genomic.fna.gz --refList GCF_008710095.1_ASM871009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008710095.1_ASM871009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:33,641] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:33,658] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:33,658] [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_008710095.1	s__Affinibrenneria salicis	100.0	1847	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Affinibrenneria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013155275.1	s__Brenneria sp013155275	81.0769	698	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
GCF_005484965.1	s__Brenneria nigrifluens	80.4298	742	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	-
GCF_017569925.1	s__Brenneria izadpanahii	80.2238	708	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291445.1	s__Brenneria goodwinii	80.0966	693	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	-
GCF_003115845.1	s__Brenneria roseae	79.8895	570	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	96.57	96.57	0.91	0.91	2	-
GCF_002812485.1	s__Dickeya fangzhongdai	79.7125	624	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCA_901472405.1	s__Serratia_B rubidaea	79.565	652	1941	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_900187015.1	s__Serratia ficaria	79.5444	670	1941	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	79.5243	637	1941	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_000738675.1	s__Serratia nematodiphila	79.5192	650	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_002220655.1	s__Serratia marcescens_K	79.4389	645	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_003812745.1	s__Serratia sp003812745	79.3902	599	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCF_013375155.1	s__Serratia ureilytica	79.3816	633	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_006715005.1	s__Serratia marcescens_J	79.3018	623	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_000406145.1	s__Dickeya dadantii	79.247	611	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	-
GCF_002291425.1	s__Gibbsiella quercinecans	79.1573	670	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gibbsiella	95.0	99.45	98.17	0.96	0.87	5	-
GCF_005491205.1	s__Chimaeribacter sp005491205	78.807	486	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:33,670] [INFO] GTDB search result was written to GCF_008710095.1_ASM871009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:33,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:33,676] [INFO] DFAST_QC result json was written to GCF_008710095.1_ASM871009v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:33,677] [INFO] DFAST_QC completed!
[2024-01-24 15:04:33,677] [INFO] Total running time: 0h1m57s