[2024-01-24 13:57:00,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference
[2024-01-24 13:57:01,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:01,629] [INFO] Task started: Prodigal
[2024-01-24 13:57:01,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg6370ef2d-5f7b-4bc4-b6fa-9ef48c03b86d/GCF_002006995.1_ASM200699v1_genomic.fna.gz | prodigal -d GCF_002006995.1_ASM200699v1_genomic.fna/cds.fna -a GCF_002006995.1_ASM200699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:14,738] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:14,739] [INFO] Task started: HMMsearch
[2024-01-24 13:57:14,739] [INFO] Running command: hmmsearch --tblout GCF_002006995.1_ASM200699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference/reference_markers.hmm GCF_002006995.1_ASM200699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:15,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:15,109] [INFO] Found 6/6 markers.
[2024-01-24 13:57:15,156] [INFO] Query marker FASTA was written to GCF_002006995.1_ASM200699v1_genomic.fna/markers.fasta
[2024-01-24 13:57:15,156] [INFO] Task started: Blastn
[2024-01-24 13:57:15,156] [INFO] Running command: blastn -query GCF_002006995.1_ASM200699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference/reference_markers.fasta -out GCF_002006995.1_ASM200699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:15,983] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:15,989] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:15,990] [INFO] Target genome list was writen to GCF_002006995.1_ASM200699v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:15,999] [INFO] Task started: fastANI
[2024-01-24 13:57:16,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg6370ef2d-5f7b-4bc4-b6fa-9ef48c03b86d/GCF_002006995.1_ASM200699v1_genomic.fna.gz --refList GCF_002006995.1_ASM200699v1_genomic.fna/target_genomes.txt --output GCF_002006995.1_ASM200699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:35,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:35,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:35,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:35,705] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:35,705] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:35,705] [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
Izhakiella australiensis	strain=D4N98	GCA_002006995.1	1926881	1926881	type	True	100.0	1634	1640	95	conclusive
Izhakiella capsodis	strain=N6PO6	GCA_900115045.1	1367852	1367852	type	True	82.5793	852	1640	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	79.0468	563	1640	95	below_threshold
Mixta calida	strain=DSM 22759	GCA_002953215.1	665913	665913	type	True	79.0414	545	1640	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	78.9566	513	1640	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	78.9212	558	1640	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.8583	498	1640	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	78.815	439	1640	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.7753	550	1640	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	78.6925	498	1640	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	78.6258	479	1640	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	78.5061	485	1640	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	78.2527	385	1640	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	78.2274	402	1640	95	below_threshold
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	78.2221	385	1640	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	78.2026	417	1640	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	78.078	423	1640	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	78.0538	425	1640	95	below_threshold
Raoultella terrigena	strain=NBRC 14941	GCA_006539725.1	577	577	type	True	78.0173	420	1640	95	below_threshold
Shimwellia blattae	strain=DSM 4481	GCA_000262305.1	563	563	type	True	77.9973	330	1640	95	below_threshold
Shimwellia blattae	strain=NBRC 105725	GCA_000327265.1	563	563	type	True	77.9561	323	1640	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	77.8587	380	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:35,707] [INFO] DFAST Taxonomy check result was written to GCF_002006995.1_ASM200699v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:35,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:35,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:35,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference/checkm_data
[2024-01-24 13:57:35,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:35,757] [INFO] Task started: CheckM
[2024-01-24 13:57:35,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002006995.1_ASM200699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002006995.1_ASM200699v1_genomic.fna/checkm_input GCF_002006995.1_ASM200699v1_genomic.fna/checkm_result
[2024-01-24 13:58:17,588] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:17,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,609] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:17,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:17,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002006995.1_ASM200699v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:17,610] [INFO] Task started: Blastn
[2024-01-24 13:58:17,610] [INFO] Running command: blastn -query GCF_002006995.1_ASM200699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25b2e885-8027-4420-a541-a11ed13a0831/dqc_reference/reference_markers_gtdb.fasta -out GCF_002006995.1_ASM200699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:18,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:18,748] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:18,748] [INFO] Target genome list was writen to GCF_002006995.1_ASM200699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:18,798] [INFO] Task started: fastANI
[2024-01-24 13:58:18,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg6370ef2d-5f7b-4bc4-b6fa-9ef48c03b86d/GCF_002006995.1_ASM200699v1_genomic.fna.gz --refList GCF_002006995.1_ASM200699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002006995.1_ASM200699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:37,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,008] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:38,008] [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_002006995.1	s__Izhakiella australiensis	100.0	1634	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115045.1	s__Izhakiella capsodis	82.5793	852	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752165.1	s__Izhakiella sp002752165	81.2273	781	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella	95.0	99.99	99.99	0.99	0.98	7	-
GCF_002953195.1	s__Mixta gaviniae	79.049	560	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.91	99.91	0.99	0.99	2	-
GCF_002953215.1	s__Mixta calida	79.029	544	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	-
GCF_003937915.1	s__Erwinia sp003937915	78.9671	558	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517625.1	s__Mixta tenebrionis	78.9237	557	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
GCF_000770305.1	s__Erwinia oleae	78.8662	503	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.06	98.06	0.89	0.89	2	-
GCF_002095385.1	s__Pantoea eucrina	78.803	439	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.84	96.54	0.93	0.90	17	-
GCF_000773975.1	s__Erwinia typographi	78.7744	563	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.41	96.41	0.95	0.95	2	-
GCF_001267535.1	s__Erwinia iniecta	78.6984	496	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_014773485.1	s__Erwinia aphidicola	78.6778	552	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_002095535.1	s__Pantoea cypripedii	78.6301	478	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCA_002359495.1	s__Pantoea sp002359495	78.6056	482	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.89	99.89	0.94	0.94	2	-
GCF_000759815.1	s__Citrobacter_A rodentium	78.2218	386	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	-
GCF_001975225.1	s__Kosakonia cowanii	78.1451	411	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	97.51	95.65	0.94	0.87	21	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	78.0415	434	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_000262305.1	s__Shimwellia blattae	77.9938	326	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	99.99	99.99	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,010] [INFO] GTDB search result was written to GCF_002006995.1_ASM200699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:38,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:38,017] [INFO] DFAST_QC result json was written to GCF_002006995.1_ASM200699v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:38,018] [INFO] DFAST_QC completed!
[2024-01-24 13:58:38,018] [INFO] Total running time: 0h1m38s