[2024-01-24 12:07:06,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,875] [INFO] DQC Reference Directory: /var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference
[2024-01-24 12:07:08,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:08,151] [INFO] Task started: Prodigal
[2024-01-24 12:07:08,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f8baa4e-6fb8-437f-a3c2-4bf3d9f7da59/GCF_018494065.1_ASM1849406v1_genomic.fna.gz | prodigal -d GCF_018494065.1_ASM1849406v1_genomic.fna/cds.fna -a GCF_018494065.1_ASM1849406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:14,902] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:14,902] [INFO] Task started: HMMsearch
[2024-01-24 12:07:14,902] [INFO] Running command: hmmsearch --tblout GCF_018494065.1_ASM1849406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference/reference_markers.hmm GCF_018494065.1_ASM1849406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:15,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:15,203] [INFO] Found 6/6 markers.
[2024-01-24 12:07:15,229] [INFO] Query marker FASTA was written to GCF_018494065.1_ASM1849406v1_genomic.fna/markers.fasta
[2024-01-24 12:07:15,230] [INFO] Task started: Blastn
[2024-01-24 12:07:15,230] [INFO] Running command: blastn -query GCF_018494065.1_ASM1849406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference/reference_markers.fasta -out GCF_018494065.1_ASM1849406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,010] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,014] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:16,014] [INFO] Target genome list was writen to GCF_018494065.1_ASM1849406v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:16,045] [INFO] Task started: fastANI
[2024-01-24 12:07:16,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f8baa4e-6fb8-437f-a3c2-4bf3d9f7da59/GCF_018494065.1_ASM1849406v1_genomic.fna.gz --refList GCF_018494065.1_ASM1849406v1_genomic.fna/target_genomes.txt --output GCF_018494065.1_ASM1849406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:27,584] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:27,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:27,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:27,599] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:27,599] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:27,599] [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
Rosenbergiella nectarea	strain=8N4	GCA_900111105.1	988801	988801	type	True	86.1072	799	987	95	below_threshold
Rosenbergiella epipactidis	strain=2.1A	GCA_018494055.1	1544694	1544694	type	True	84.6278	765	987	95	below_threshold
Rosenbergiella collisarenosi	strain=8.8A	GCA_018494085.1	1544695	1544695	type	True	82.0727	613	987	95	below_threshold
Rosenbergiella australiborealis	strain=CdVSA20.1	GCA_018494035.1	1544696	1544696	type	True	81.6061	535	987	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.0436	103	987	95	below_threshold
Tatumella citrea	strain=DSM 13699	GCA_002163585.1	53336	53336	type	True	78.7096	160	987	95	below_threshold
Buttiauxella ferragutiae	strain=ATCC 51602	GCA_001654915.1	82989	82989	type	True	78.4077	99	987	95	below_threshold
Pantoea ananatis	strain=LMG 2665	GCA_000661975.1	553	553	type	True	78.4062	135	987	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	78.326	95	987	95	below_threshold
Pantoea ananatis	strain=LMG 2665	GCA_000710035.2	553	553	type	True	78.2897	134	987	95	below_threshold
Moellerella wisconsensis	strain=NCTC12132	GCA_900706815.1	158849	158849	type	True	78.2762	78	987	95	below_threshold
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	78.157	104	987	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	78.0921	136	987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:27,601] [INFO] DFAST Taxonomy check result was written to GCF_018494065.1_ASM1849406v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:27,601] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:27,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:27,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference/checkm_data
[2024-01-24 12:07:27,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:27,634] [INFO] Task started: CheckM
[2024-01-24 12:07:27,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018494065.1_ASM1849406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018494065.1_ASM1849406v1_genomic.fna/checkm_input GCF_018494065.1_ASM1849406v1_genomic.fna/checkm_result
[2024-01-24 12:07:54,558] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:54,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,586] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:54,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:54,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018494065.1_ASM1849406v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:54,588] [INFO] Task started: Blastn
[2024-01-24 12:07:54,588] [INFO] Running command: blastn -query GCF_018494065.1_ASM1849406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3b1c02-3247-4ecc-a6d3-0bbfe730cee6/dqc_reference/reference_markers_gtdb.fasta -out GCF_018494065.1_ASM1849406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:55,735] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:55,739] [INFO] Selected 8 target genomes.
[2024-01-24 12:07:55,739] [INFO] Target genome list was writen to GCF_018494065.1_ASM1849406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:55,745] [INFO] Task started: fastANI
[2024-01-24 12:07:55,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f8baa4e-6fb8-437f-a3c2-4bf3d9f7da59/GCF_018494065.1_ASM1849406v1_genomic.fna.gz --refList GCF_018494065.1_ASM1849406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018494065.1_ASM1849406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:01,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:01,604] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:01,604] [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_018494065.1	s__Rosenbergiella sp018494065	100.0	985	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111105.1	s__Rosenbergiella nectarea	86.0926	800	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
GCF_018494055.1	s__Rosenbergiella epipactidis	84.6278	765	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.28	95.56	0.88	0.85	5	-
GCF_018494085.1	s__Rosenbergiella collisarenosi	82.0626	615	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	99.00	99.00	0.87	0.87	2	-
GCF_018494035.1	s__Rosenbergiella australiborealis	81.6001	536	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963575.1	s__Cedecea michiganensis_A	78.5663	85	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517405.1	s__Erwinia_B gerundensis	78.5125	125	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia_B	95.0	98.84	98.67	0.95	0.94	8	-
GCF_018257575.1	s__Tatumella sp018257575	78.4734	171	987	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.64	99.52	0.95	0.93	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:01,606] [INFO] GTDB search result was written to GCF_018494065.1_ASM1849406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:01,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:01,610] [INFO] DFAST_QC result json was written to GCF_018494065.1_ASM1849406v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:01,610] [INFO] DFAST_QC completed!
[2024-01-24 12:08:01,610] [INFO] Total running time: 0h0m55s