[2024-01-24 14:28:02,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference
[2024-01-24 14:28:04,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,030] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg183015c6-9616-416e-a349-659cdda37133/GCF_000280495.2_ASM28049v2_genomic.fna.gz | prodigal -d GCF_000280495.2_ASM28049v2_genomic.fna/cds.fna -a GCF_000280495.2_ASM28049v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:21,677] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:21,678] [INFO] Task started: HMMsearch
[2024-01-24 14:28:21,678] [INFO] Running command: hmmsearch --tblout GCF_000280495.2_ASM28049v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference/reference_markers.hmm GCF_000280495.2_ASM28049v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:22,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:22,074] [INFO] Found 6/6 markers.
[2024-01-24 14:28:22,124] [INFO] Query marker FASTA was written to GCF_000280495.2_ASM28049v2_genomic.fna/markers.fasta
[2024-01-24 14:28:22,124] [INFO] Task started: Blastn
[2024-01-24 14:28:22,124] [INFO] Running command: blastn -query GCF_000280495.2_ASM28049v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference/reference_markers.fasta -out GCF_000280495.2_ASM28049v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:23,059] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:23,063] [INFO] Selected 23 target genomes.
[2024-01-24 14:28:23,063] [INFO] Target genome list was writen to GCF_000280495.2_ASM28049v2_genomic.fna/target_genomes.txt
[2024-01-24 14:28:23,098] [INFO] Task started: fastANI
[2024-01-24 14:28:23,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg183015c6-9616-416e-a349-659cdda37133/GCF_000280495.2_ASM28049v2_genomic.fna.gz --refList GCF_000280495.2_ASM28049v2_genomic.fna/target_genomes.txt --output GCF_000280495.2_ASM28049v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:48,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:48,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:48,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:48,152] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:48,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:48,153] [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
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	95.7256	1686	2039	95	conclusive
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	95.7251	1707	2039	95	conclusive
Kosakonia oryziphila	strain=REICA_142	GCA_900094795.1	1005667	1005667	type	True	93.2297	1330	2039	95	below_threshold
Kosakonia arachidis	strain=Ah-143	GCA_900116535.1	551989	551989	type	True	92.7772	1480	2039	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	85.1585	1289	2039	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	85.0084	1274	2039	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	84.1333	1240	2039	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	83.7777	1170	2039	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.5932	928	2039	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.589	927	2039	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.5611	913	2039	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.2819	878	2039	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.2448	918	2039	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	81.151	872	2039	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	79.3576	594	2039	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	79.2643	602	2039	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	78.795	517	2039	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	78.5508	505	2039	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	78.5264	476	2039	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	78.3719	483	2039	95	below_threshold
Edwardsiella piscicida	strain=ACC35.1	GCA_001896205.1	1263550	1263550	reftype	True	78.0154	351	2039	95	below_threshold
Pseudoduganella ginsengisoli	strain=KCTC 42409	GCA_009720865.1	1462440	1462440	type	True	74.966	52	2039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:48,154] [INFO] DFAST Taxonomy check result was written to GCF_000280495.2_ASM28049v2_genomic.fna/tc_result.tsv
[2024-01-24 14:28:48,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:48,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:48,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference/checkm_data
[2024-01-24 14:28:48,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:48,216] [INFO] Task started: CheckM
[2024-01-24 14:28:48,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000280495.2_ASM28049v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000280495.2_ASM28049v2_genomic.fna/checkm_input GCF_000280495.2_ASM28049v2_genomic.fna/checkm_result
[2024-01-24 14:29:40,833] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:40,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:40,857] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:40,857] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:40,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000280495.2_ASM28049v2_genomic.fna/markers.fasta)
[2024-01-24 14:29:40,858] [INFO] Task started: Blastn
[2024-01-24 14:29:40,859] [INFO] Running command: blastn -query GCF_000280495.2_ASM28049v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg48477cbf-b3f4-4345-8986-c5066ea94175/dqc_reference/reference_markers_gtdb.fasta -out GCF_000280495.2_ASM28049v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:42,093] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:42,097] [INFO] Selected 18 target genomes.
[2024-01-24 14:29:42,097] [INFO] Target genome list was writen to GCF_000280495.2_ASM28049v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:42,127] [INFO] Task started: fastANI
[2024-01-24 14:29:42,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg183015c6-9616-416e-a349-659cdda37133/GCF_000280495.2_ASM28049v2_genomic.fna.gz --refList GCF_000280495.2_ASM28049v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000280495.2_ASM28049v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:04,416] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:04,436] [INFO] Found 18 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:30:04,436] [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_000280495.2	s__Kosakonia radicincitans	100.0	2037	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	inconclusive
GCA_009929615.1	s__Frisingicoccus sp009929615	97.6158	61	2039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.91	99.91	0.88	0.88	2	inconclusive
GCF_001658025.2	s__Kosakonia oryzae	95.7271	1708	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	98.47	96.95	0.97	0.93	3	-
GCA_900109485.1	s__Kosakonia sacchari_B	95.5795	1644	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7228	98.05	98.05	0.93	0.93	2	-
GCA_018261615.1	s__Kosakonia sp018261615	93.6588	1347	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094795.1	s__Kosakonia oryziphila	93.2066	1332	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116535.1	s__Kosakonia arachidis	92.7771	1480	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000300455.3	s__Kosakonia sacchari	85.1536	1290	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.35	95.81	0.96	0.92	5	-
GCF_009363175.1	s__Citrobacter_A telavivensis	82.6737	949	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006711645.1	s__Klebsiella electrica	82.2507	953	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.88	98.54	0.89	0.85	7	-
GCF_014168815.1	s__Kluyvera ascorbata_B	82.2449	904	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCF_000025565.1	s__Enterobacter cloacae	82.1918	987	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	-
GCF_001521715.1	s__Enterobacter asburiae	81.7254	920	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_002939185.1	s__Enterobacter sichuanensis	81.2483	924	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_007680145.1	s__Pseudescherichia sp002298805	80.9891	877	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.55	96.56	0.95	0.92	13	-
GCF_005671395.1	s__Jejubacter calystegiae	79.5545	612	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	98.55	98.55	0.90	0.90	2	-
GCF_002095535.1	s__Pantoea cypripedii	79.3447	596	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001922585.1	s__1-19 sp001922585	78.5161	430	2039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__1-19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:04,438] [INFO] GTDB search result was written to GCF_000280495.2_ASM28049v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:04,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:04,442] [INFO] DFAST_QC result json was written to GCF_000280495.2_ASM28049v2_genomic.fna/dqc_result.json
[2024-01-24 14:30:04,443] [INFO] DFAST_QC completed!
[2024-01-24 14:30:04,443] [INFO] Total running time: 0h2m2s