[2024-01-24 12:13:06,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:06,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:06,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference
[2024-01-24 12:13:07,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,571] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,571] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5060c19-6660-456c-8745-a39f1ad843a1/GCF_004295645.1_ASM429564v1_genomic.fna.gz | prodigal -d GCF_004295645.1_ASM429564v1_genomic.fna/cds.fna -a GCF_004295645.1_ASM429564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:18,080] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:18,081] [INFO] Task started: HMMsearch
[2024-01-24 12:13:18,081] [INFO] Running command: hmmsearch --tblout GCF_004295645.1_ASM429564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference/reference_markers.hmm GCF_004295645.1_ASM429564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:18,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:18,313] [INFO] Found 6/6 markers.
[2024-01-24 12:13:18,353] [INFO] Query marker FASTA was written to GCF_004295645.1_ASM429564v1_genomic.fna/markers.fasta
[2024-01-24 12:13:18,353] [INFO] Task started: Blastn
[2024-01-24 12:13:18,353] [INFO] Running command: blastn -query GCF_004295645.1_ASM429564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference/reference_markers.fasta -out GCF_004295645.1_ASM429564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:19,144] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:19,148] [INFO] Selected 13 target genomes.
[2024-01-24 12:13:19,148] [INFO] Target genome list was writen to GCF_004295645.1_ASM429564v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:19,157] [INFO] Task started: fastANI
[2024-01-24 12:13:19,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5060c19-6660-456c-8745-a39f1ad843a1/GCF_004295645.1_ASM429564v1_genomic.fna.gz --refList GCF_004295645.1_ASM429564v1_genomic.fna/target_genomes.txt --output GCF_004295645.1_ASM429564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:29,998] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:29,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:29,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:30,010] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:30,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:30,010] [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
Jinshanibacter zhutongyuii	strain=CF-458	GCA_004295645.1	2498113	2498113	type	True	100.0	1538	1543	95	conclusive
Jinshanibacter allomyrinae	strain=BWR-B9	GCA_016649425.1	2791986	2791986	type	True	91.551	1265	1543	95	below_threshold
Pragia fontium	strain=DSM 5563	GCA_004959795.1	82985	82985	type	True	80.3482	639	1543	95	below_threshold
Pragia fontium	strain=DSM 5563	GCA_900112475.1	82985	82985	type	True	80.3226	643	1543	95	below_threshold
Budvicia aquatica	strain=NCTC12282	GCA_900706715.1	82979	82979	type	True	79.6609	576	1543	95	below_threshold
Budvicia aquatica	strain=DSM 5075	GCA_000427805.1	82979	82979	type	True	79.4168	582	1543	95	below_threshold
Budvicia diplopodorum	strain=D9	GCA_009800925.1	1119056	1119056	type	True	79.2716	482	1543	95	below_threshold
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	78.7878	408	1543	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.7328	152	1543	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.5311	194	1543	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.4711	152	1543	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	78.2274	364	1543	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	77.732	153	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:30,012] [INFO] DFAST Taxonomy check result was written to GCF_004295645.1_ASM429564v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:30,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:30,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:30,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference/checkm_data
[2024-01-24 12:13:30,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:30,056] [INFO] Task started: CheckM
[2024-01-24 12:13:30,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004295645.1_ASM429564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004295645.1_ASM429564v1_genomic.fna/checkm_input GCF_004295645.1_ASM429564v1_genomic.fna/checkm_result
[2024-01-24 12:14:04,962] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:04,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:04,985] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:04,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:04,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004295645.1_ASM429564v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:04,986] [INFO] Task started: Blastn
[2024-01-24 12:14:04,986] [INFO] Running command: blastn -query GCF_004295645.1_ASM429564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0229d1c-0e86-484c-b869-d4addb97ad27/dqc_reference/reference_markers_gtdb.fasta -out GCF_004295645.1_ASM429564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:06,154] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:06,158] [INFO] Selected 7 target genomes.
[2024-01-24 12:14:06,158] [INFO] Target genome list was writen to GCF_004295645.1_ASM429564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:06,163] [INFO] Task started: fastANI
[2024-01-24 12:14:06,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5060c19-6660-456c-8745-a39f1ad843a1/GCF_004295645.1_ASM429564v1_genomic.fna.gz --refList GCF_004295645.1_ASM429564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004295645.1_ASM429564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:13,946] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:13,952] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:13,952] [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_004295645.1	s__Limnobaculum zhutongyuii	100.0	1539	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_016649425.1	s__Limnobaculum allomyrinae	91.5601	1264	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013394855.1	s__Limnobaculum xujianqingii	90.9516	1320	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	-
GCF_003096015.2	s__Limnobaculum parvum	87.6539	1053	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112475.1	s__Pragia fontium	80.32	643	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	-
GCF_000427805.1	s__Budvicia aquatica	79.411	584	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	99.94	99.91	1.00	1.00	3	-
GCF_009800925.1	s__Budvicia diplopodorum	79.2824	480	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:13,954] [INFO] GTDB search result was written to GCF_004295645.1_ASM429564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:13,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:13,958] [INFO] DFAST_QC result json was written to GCF_004295645.1_ASM429564v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:13,958] [INFO] DFAST_QC completed!
[2024-01-24 12:14:13,958] [INFO] Total running time: 0h1m8s