[2023-06-29 02:58:02,543] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:58:02,546] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:58:02,546] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference
[2023-06-29 02:58:04,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:58:04,908] [INFO] Task started: Prodigal
[2023-06-29 02:58:04,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg652945ce-5c8f-4ef7-8cf9-c01871fe850d/GCA_015655145.1_ASM1565514v1_genomic.fna.gz | prodigal -d GCA_015655145.1_ASM1565514v1_genomic.fna/cds.fna -a GCA_015655145.1_ASM1565514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:58:15,951] [INFO] Task succeeded: Prodigal
[2023-06-29 02:58:15,951] [INFO] Task started: HMMsearch
[2023-06-29 02:58:15,951] [INFO] Running command: hmmsearch --tblout GCA_015655145.1_ASM1565514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference/reference_markers.hmm GCA_015655145.1_ASM1565514v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:58:16,209] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:58:16,211] [INFO] Found 6/6 markers.
[2023-06-29 02:58:16,248] [INFO] Query marker FASTA was written to GCA_015655145.1_ASM1565514v1_genomic.fna/markers.fasta
[2023-06-29 02:58:16,249] [INFO] Task started: Blastn
[2023-06-29 02:58:16,249] [INFO] Running command: blastn -query GCA_015655145.1_ASM1565514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference/reference_markers.fasta -out GCA_015655145.1_ASM1565514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:58:17,100] [INFO] Task succeeded: Blastn
[2023-06-29 02:58:17,105] [INFO] Selected 23 target genomes.
[2023-06-29 02:58:17,105] [INFO] Target genome list was writen to GCA_015655145.1_ASM1565514v1_genomic.fna/target_genomes.txt
[2023-06-29 02:58:17,115] [INFO] Task started: fastANI
[2023-06-29 02:58:17,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg652945ce-5c8f-4ef7-8cf9-c01871fe850d/GCA_015655145.1_ASM1565514v1_genomic.fna.gz --refList GCA_015655145.1_ASM1565514v1_genomic.fna/target_genomes.txt --output GCA_015655145.1_ASM1565514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:58:34,016] [INFO] Task succeeded: fastANI
[2023-06-29 02:58:34,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:58:34,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:58:34,046] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:58:34,046] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:58:34,046] [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
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	78.9896	435	1313	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	78.8759	357	1313	95	below_threshold
[Pantoea] beijingensis	strain=LMG 27579	GCA_004022165.1	1324864	1324864	type	True	78.8623	360	1313	95	below_threshold
Mixta calida	strain=DSM 22759	GCA_002953215.1	665913	665913	type	True	78.5143	353	1313	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	78.4776	336	1313	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	78.4301	344	1313	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	78.3526	343	1313	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	78.1582	320	1313	95	below_threshold
Izhakiella australiensis	strain=D4N98	GCA_002006995.1	1926881	1926881	type	True	77.9499	252	1313	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	77.8912	311	1313	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	77.8753	355	1313	95	below_threshold
Erwinia psidii	strain=IBSBF 435	GCA_003846135.1	69224	69224	type	True	77.6823	287	1313	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	77.4858	192	1313	95	below_threshold
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	77.477	229	1313	95	below_threshold
Mangrovibacter phragmitis	strain=MP23	GCA_001655675.1	1691903	1691903	type	True	77.3756	194	1313	95	below_threshold
Mangrovibacter plantisponsor	strain=DSM 19579	GCA_003182475.1	451513	451513	type	True	77.3237	193	1313	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	77.2596	223	1313	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	77.1604	216	1313	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	77.14	217	1313	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	77.1164	208	1313	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	77.078	203	1313	95	below_threshold
Atlantibacter hermannii	strain=NBRC 105704	GCA_000248015.2	565	565	type	True	77.0627	217	1313	95	below_threshold
Rahnella bruchi	strain=DSM 27398	GCA_003614975.1	1510573	1510573	type	True	76.9413	191	1313	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:58:34,048] [INFO] DFAST Taxonomy check result was written to GCA_015655145.1_ASM1565514v1_genomic.fna/tc_result.tsv
[2023-06-29 02:58:34,049] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:58:34,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:58:34,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference/checkm_data
[2023-06-29 02:58:34,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:58:34,093] [INFO] Task started: CheckM
[2023-06-29 02:58:34,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015655145.1_ASM1565514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015655145.1_ASM1565514v1_genomic.fna/checkm_input GCA_015655145.1_ASM1565514v1_genomic.fna/checkm_result
[2023-06-29 02:59:10,658] [INFO] Task succeeded: CheckM
[2023-06-29 02:59:10,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:59:10,679] [INFO] ===== Completeness check finished =====
[2023-06-29 02:59:10,679] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:59:10,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015655145.1_ASM1565514v1_genomic.fna/markers.fasta)
[2023-06-29 02:59:10,680] [INFO] Task started: Blastn
[2023-06-29 02:59:10,681] [INFO] Running command: blastn -query GCA_015655145.1_ASM1565514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc1bf8ca-455e-4bf2-ad87-4bd6a1eb3e15/dqc_reference/reference_markers_gtdb.fasta -out GCA_015655145.1_ASM1565514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:59:11,993] [INFO] Task succeeded: Blastn
[2023-06-29 02:59:12,003] [INFO] Selected 21 target genomes.
[2023-06-29 02:59:12,003] [INFO] Target genome list was writen to GCA_015655145.1_ASM1565514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:59:12,024] [INFO] Task started: fastANI
[2023-06-29 02:59:12,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg652945ce-5c8f-4ef7-8cf9-c01871fe850d/GCA_015655145.1_ASM1565514v1_genomic.fna.gz --refList GCA_015655145.1_ASM1565514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015655145.1_ASM1565514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:59:28,362] [INFO] Task succeeded: fastANI
[2023-06-29 02:59:28,391] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 02:59:28,391] [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_015655145.1	s__JAATFO01 sp015655145	100.0	1303	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__JAATFO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013285385.1	s__PD-1 sp013285385	79.3391	458	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__PD-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267535.1	s__Erwinia iniecta	78.9896	435	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_004022165.1	s__Erwinia beijingensis	78.8624	360	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.78	99.57	0.98	0.97	3	-
GCF_017875465.1	s__Erwinia toletana	78.7026	468	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.93	99.93	0.98	0.98	2	-
GCF_002895925.1	s__Mixta theicola	78.6271	366	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953215.1	s__Mixta calida	78.5033	354	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	-
GCF_006517625.1	s__Mixta tenebrionis	78.3455	343	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
GCF_900604315.1	s__Pantoea mediterraneensis	78.2682	331	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003512805.1	s__Erwinia sp003512805	78.2143	191	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599885.1	s__Erwinia sp000599885	78.1463	315	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295515.1	s__Erwinia endophytica	78.0236	348	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196615.1	s__Erwinia billingiae	77.9876	360	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	97.77	97.43	0.91	0.82	7	-
GCF_008632075.1	s__Pantoea sp008632075	77.9509	329	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.47	99.36	0.95	0.94	34	-
GCF_014838825.1	s__Erwinia persicina_A	77.9209	353	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCA_019132875.1	s__Erwinia sp019132875	77.8912	311	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571305.1	s__Erwinia persicina	77.8753	355	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.41	99.25	0.96	0.94	13	-
GCF_003818135.1	s__Buttiauxella warmboldiae	77.4865	230	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655675.1	s__Mangrovibacter phragmitis	77.3756	194	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mangrovibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182475.1	s__Mangrovibacter plantisponsor	77.3091	194	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mangrovibacter	95.0	98.41	98.41	0.89	0.89	2	-
GCA_900635495.1	s__Atlantibacter hermannii	77.1512	214	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
--------------------------------------------------------------------------------
[2023-06-29 02:59:28,393] [INFO] GTDB search result was written to GCA_015655145.1_ASM1565514v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:59:28,394] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:59:28,402] [INFO] DFAST_QC result json was written to GCA_015655145.1_ASM1565514v1_genomic.fna/dqc_result.json
[2023-06-29 02:59:28,402] [INFO] DFAST_QC completed!
[2023-06-29 02:59:28,402] [INFO] Total running time: 0h1m26s