[2024-01-24 11:34:43,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference
[2024-01-24 11:34:44,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,540] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ba8fe55-da08-48e2-aa6c-48b4837c6ad8/GCF_010131535.1_ASM1013153v1_genomic.fna.gz | prodigal -d GCF_010131535.1_ASM1013153v1_genomic.fna/cds.fna -a GCF_010131535.1_ASM1013153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:00,425] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:00,426] [INFO] Task started: HMMsearch
[2024-01-24 11:35:00,426] [INFO] Running command: hmmsearch --tblout GCF_010131535.1_ASM1013153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference/reference_markers.hmm GCF_010131535.1_ASM1013153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:00,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:00,794] [INFO] Found 6/6 markers.
[2024-01-24 11:35:00,840] [INFO] Query marker FASTA was written to GCF_010131535.1_ASM1013153v1_genomic.fna/markers.fasta
[2024-01-24 11:35:00,841] [INFO] Task started: Blastn
[2024-01-24 11:35:00,841] [INFO] Running command: blastn -query GCF_010131535.1_ASM1013153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference/reference_markers.fasta -out GCF_010131535.1_ASM1013153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:01,675] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:01,678] [INFO] Selected 21 target genomes.
[2024-01-24 11:35:01,678] [INFO] Target genome list was writen to GCF_010131535.1_ASM1013153v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:01,725] [INFO] Task started: fastANI
[2024-01-24 11:35:01,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba8fe55-da08-48e2-aa6c-48b4837c6ad8/GCF_010131535.1_ASM1013153v1_genomic.fna.gz --refList GCF_010131535.1_ASM1013153v1_genomic.fna/target_genomes.txt --output GCF_010131535.1_ASM1013153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:21,481] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:21,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:21,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:21,496] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:21,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:21,497] [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
Sodalis ligni	strain=dw23	GCA_016865525.2	2697027	2697027	type	True	81.1053	1022	1853	95	below_threshold
Sodalis ligni	strain=159R	GCA_004346745.1	2697027	2697027	type	True	81.0997	1035	1853	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	79.0232	636	1853	95	below_threshold
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	78.9802	654	1853	95	below_threshold
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	78.7912	596	1853	95	below_threshold
Serratia nematodiphila	strain=CGMCC 1.6853	GCA_900101535.1	458197	458197	suspected-type	True	78.7806	587	1853	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7437	599	1853	95	below_threshold
Serratia surfactantfaciens	strain=YD25	GCA_001642805.2	2741499	2741499	type	True	78.7151	581	1853	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.6955	567	1853	95	below_threshold
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	78.6617	516	1853	95	below_threshold
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	78.6216	533	1853	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	78.1463	491	1853	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	78.0935	490	1853	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	78.0773	501	1853	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_003666235.1	1109412	1109412	type	True	77.9528	397	1853	95	below_threshold
Lonsdalea britannica	strain=LMG 26267	GCA_002111595.1	1082704	1082704	type	True	77.9307	315	1853	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_002291445.1	1109412	1109412	type	True	77.9168	399	1853	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.7582	379	1853	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:21,500] [INFO] DFAST Taxonomy check result was written to GCF_010131535.1_ASM1013153v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:21,500] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:21,500] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:21,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference/checkm_data
[2024-01-24 11:35:21,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:21,559] [INFO] Task started: CheckM
[2024-01-24 11:35:21,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010131535.1_ASM1013153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010131535.1_ASM1013153v1_genomic.fna/checkm_input GCF_010131535.1_ASM1013153v1_genomic.fna/checkm_result
[2024-01-24 11:36:07,639] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:07,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:07,657] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:07,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:07,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010131535.1_ASM1013153v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:07,658] [INFO] Task started: Blastn
[2024-01-24 11:36:07,658] [INFO] Running command: blastn -query GCF_010131535.1_ASM1013153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg774f1d13-e627-4c40-86e8-96cb0bf08cf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_010131535.1_ASM1013153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:08,782] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:08,786] [INFO] Selected 12 target genomes.
[2024-01-24 11:36:08,786] [INFO] Target genome list was writen to GCF_010131535.1_ASM1013153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:08,796] [INFO] Task started: fastANI
[2024-01-24 11:36:08,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba8fe55-da08-48e2-aa6c-48b4837c6ad8/GCF_010131535.1_ASM1013153v1_genomic.fna.gz --refList GCF_010131535.1_ASM1013153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010131535.1_ASM1013153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:21,069] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:21,085] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:21,085] [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_010131535.1	s__Acerihabitans arboris	100.0	1851	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015654925.1	s__Acerihabitans sp015654925	83.3413	1089	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865525.2	s__Acerihabitans sp004346745	81.1107	1022	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	98.11	98.11	0.88	0.88	2	-
GCF_018449575.1	s__Acerihabitans sp018449575	81.0446	966	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654745.1	s__Acerihabitans sp015654745	80.2731	783	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143145.1	s__SoCistrobi sp900143145	79.455	442	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__SoCistrobi	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343195.1	s__Biostraticola tofi	79.3165	563	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Biostraticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	78.8474	565	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
GCF_000738675.1	s__Serratia nematodiphila	78.809	592	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_018336935.1	s__Serratia plymuthica_B	78.3348	545	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520015.2	s__Chania multitudinisentens	77.6426	315	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000496755.2	s__Serratia_A sp000496755	77.6418	200	1853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:21,086] [INFO] GTDB search result was written to GCF_010131535.1_ASM1013153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:21,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:21,090] [INFO] DFAST_QC result json was written to GCF_010131535.1_ASM1013153v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:21,090] [INFO] DFAST_QC completed!
[2024-01-24 11:36:21,090] [INFO] Total running time: 0h1m38s