[2024-01-24 13:32:34,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference
[2024-01-24 13:32:35,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:35,835] [INFO] Task started: Prodigal
[2024-01-24 13:32:35,836] [INFO] Running command: gunzip -c /var/lib/cwl/stgc67ae7c3-a2b0-4ae1-827c-f4a8c1bd910a/GCF_001050515.1_ASM105051v1_genomic.fna.gz | prodigal -d GCF_001050515.1_ASM105051v1_genomic.fna/cds.fna -a GCF_001050515.1_ASM105051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:46,536] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:46,537] [INFO] Task started: HMMsearch
[2024-01-24 13:32:46,537] [INFO] Running command: hmmsearch --tblout GCF_001050515.1_ASM105051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference/reference_markers.hmm GCF_001050515.1_ASM105051v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:46,961] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:46,963] [INFO] Found 6/6 markers.
[2024-01-24 13:32:47,007] [INFO] Query marker FASTA was written to GCF_001050515.1_ASM105051v1_genomic.fna/markers.fasta
[2024-01-24 13:32:47,008] [INFO] Task started: Blastn
[2024-01-24 13:32:47,008] [INFO] Running command: blastn -query GCF_001050515.1_ASM105051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference/reference_markers.fasta -out GCF_001050515.1_ASM105051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,881] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:47,881] [INFO] Target genome list was writen to GCF_001050515.1_ASM105051v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:47,888] [INFO] Task started: fastANI
[2024-01-24 13:32:47,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgc67ae7c3-a2b0-4ae1-827c-f4a8c1bd910a/GCF_001050515.1_ASM105051v1_genomic.fna.gz --refList GCF_001050515.1_ASM105051v1_genomic.fna/target_genomes.txt --output GCF_001050515.1_ASM105051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:02,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:02,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:02,925] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:02,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:02,925] [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 piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	100.0	1291	1295	95	conclusive
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	89.4191	1104	1295	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	86.8694	996	1295	95	below_threshold
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	85.6085	962	1295	95	below_threshold
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	85.6005	969	1295	95	below_threshold
Erwinia amylovora	strain=type strain: CFBP 1232	GCA_000367625.2	552	552	type	True	85.5975	962	1295	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	81.8132	813	1295	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.6833	581	1295	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	78.8269	395	1295	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.6541	374	1295	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.4444	364	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,927] [INFO] DFAST Taxonomy check result was written to GCF_001050515.1_ASM105051v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:02,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:02,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:02,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference/checkm_data
[2024-01-24 13:33:02,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:02,972] [INFO] Task started: CheckM
[2024-01-24 13:33:02,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050515.1_ASM105051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050515.1_ASM105051v1_genomic.fna/checkm_input GCF_001050515.1_ASM105051v1_genomic.fna/checkm_result
[2024-01-24 13:33:40,583] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:40,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:40,606] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:40,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:40,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050515.1_ASM105051v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:40,607] [INFO] Task started: Blastn
[2024-01-24 13:33:40,607] [INFO] Running command: blastn -query GCF_001050515.1_ASM105051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d422aea-5b35-4105-b81d-20e2c97b23e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050515.1_ASM105051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:41,699] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:41,703] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:41,703] [INFO] Target genome list was writen to GCF_001050515.1_ASM105051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:41,724] [INFO] Task started: fastANI
[2024-01-24 13:33:41,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgc67ae7c3-a2b0-4ae1-827c-f4a8c1bd910a/GCF_001050515.1_ASM105051v1_genomic.fna.gz --refList GCF_001050515.1_ASM105051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001050515.1_ASM105051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:55,618] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:55,629] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:55,630] [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_001050515.1	s__Erwinia piriflorinigrans	100.0	1291	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000026185.1	s__Erwinia tasmaniensis	89.4191	1104	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026985.1	s__Erwinia pyrifoliae	86.8663	994	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.33	98.13	0.97	0.93	4	-
GCF_017161565.1	s__Erwinia amylovora	85.6088	969	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.73	98.13	0.99	0.95	141	-
GCF_014773485.1	s__Erwinia aphidicola	81.8611	798	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_012271765.1	s__Erwinia rhapontici	81.3877	787	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_014838825.1	s__Erwinia persicina_A	81.2028	761	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCF_009738185.1	s__Erwinia sp009738185	81.1768	774	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.50	99.50	0.98	0.98	2	-
GCF_003751505.1	s__Erwinia sp003751505	80.8863	689	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909495.1	s__Erwinia coffeiphila	80.7171	685	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.75	96.67	0.88	0.87	4	-
GCF_014155765.1	s__Pantoea dispersa	78.9715	529	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCF_018323985.1	s__Enterobacter_D kobei_A	78.672	367	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	99.37	98.44	0.98	0.93	6	-
GCF_000735365.1	s__Kluyvera ascorbata	78.3289	333	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCF_005843885.1	s__Escherichia sp005843885	78.1159	314	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,631] [INFO] GTDB search result was written to GCF_001050515.1_ASM105051v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:55,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:55,638] [INFO] DFAST_QC result json was written to GCF_001050515.1_ASM105051v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:55,638] [INFO] DFAST_QC completed!
[2024-01-24 13:33:55,639] [INFO] Total running time: 0h1m21s