[2024-01-25 17:38:50,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:50,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:50,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference
[2024-01-25 17:38:51,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:51,803] [INFO] Task started: Prodigal
[2024-01-25 17:38:51,803] [INFO] Running command: gunzip -c /var/lib/cwl/stgc591da2a-ec60-47d4-845c-4354fb62be3b/GCF_000749865.1_ASM74986v1_genomic.fna.gz | prodigal -d GCF_000749865.1_ASM74986v1_genomic.fna/cds.fna -a GCF_000749865.1_ASM74986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:03,414] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:03,415] [INFO] Task started: HMMsearch
[2024-01-25 17:39:03,415] [INFO] Running command: hmmsearch --tblout GCF_000749865.1_ASM74986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference/reference_markers.hmm GCF_000749865.1_ASM74986v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:03,699] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:03,702] [INFO] Found 6/6 markers.
[2024-01-25 17:39:03,742] [INFO] Query marker FASTA was written to GCF_000749865.1_ASM74986v1_genomic.fna/markers.fasta
[2024-01-25 17:39:03,742] [INFO] Task started: Blastn
[2024-01-25 17:39:03,742] [INFO] Running command: blastn -query GCF_000749865.1_ASM74986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference/reference_markers.fasta -out GCF_000749865.1_ASM74986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:04,606] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:04,609] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:04,609] [INFO] Target genome list was writen to GCF_000749865.1_ASM74986v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:04,612] [INFO] Task started: fastANI
[2024-01-25 17:39:04,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc591da2a-ec60-47d4-845c-4354fb62be3b/GCF_000749865.1_ASM74986v1_genomic.fna.gz --refList GCF_000749865.1_ASM74986v1_genomic.fna/target_genomes.txt --output GCF_000749865.1_ASM74986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:16,631] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:16,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:16,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:16,639] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:39:16,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:16,639] [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
Pectobacterium wasabiae	strain=NCPPB 3701	GCA_000749865.1	55208	55208	type	True	100.0	1644	1646	95	conclusive
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	99.9951	1646	1646	95	conclusive
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	99.9789	1630	1646	95	conclusive
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_001742145.1	1905730	1905730	type	True	93.999	1450	1646	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_000757625.1	1905730	1905730	type	True	93.969	1441	1646	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	88.623	1176	1646	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.0076	1234	1646	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.3288	407	1646	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.2625	415	1646	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.1169	392	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:16,641] [INFO] DFAST Taxonomy check result was written to GCF_000749865.1_ASM74986v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:16,641] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:16,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:16,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference/checkm_data
[2024-01-25 17:39:16,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:16,692] [INFO] Task started: CheckM
[2024-01-25 17:39:16,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000749865.1_ASM74986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000749865.1_ASM74986v1_genomic.fna/checkm_input GCF_000749865.1_ASM74986v1_genomic.fna/checkm_result
[2024-01-25 17:39:54,199] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:54,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:54,217] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:54,217] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:54,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000749865.1_ASM74986v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:54,218] [INFO] Task started: Blastn
[2024-01-25 17:39:54,218] [INFO] Running command: blastn -query GCF_000749865.1_ASM74986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6041da-cb8b-4905-92ab-aa246b8241c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000749865.1_ASM74986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:55,612] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:55,614] [INFO] Selected 9 target genomes.
[2024-01-25 17:39:55,614] [INFO] Target genome list was writen to GCF_000749865.1_ASM74986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:55,622] [INFO] Task started: fastANI
[2024-01-25 17:39:55,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgc591da2a-ec60-47d4-845c-4354fb62be3b/GCF_000749865.1_ASM74986v1_genomic.fna.gz --refList GCF_000749865.1_ASM74986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000749865.1_ASM74986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:08,175] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:08,182] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:08,182] [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_001742185.1	s__Pectobacterium wasabiae	99.9951	1646	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	conclusive
GCF_001742145.1	s__Pectobacterium parmentieri	93.9886	1451	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.20	98.87	0.95	0.90	33	-
GCF_012427845.1	s__Pectobacterium punjabense	91.1863	1305	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	-
GCF_005497185.1	s__Pectobacterium polonicum	91.0291	1333	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847345.1	s__Pectobacterium peruviense	90.1872	1231	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.76	97.64	0.96	0.93	5	-
GCF_019056595.1	s__Pectobacterium atrosepticum	89.9989	1285	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	-
GCF_000749845.1	s__Pectobacterium betavasculorum	89.2455	1199	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
GCF_004137795.1	s__Pectobacterium zantedeschiae	89.2263	1331	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	-
GCF_000754695.1	s__Pectobacterium brasiliense	88.8202	1264	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:08,183] [INFO] GTDB search result was written to GCF_000749865.1_ASM74986v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:08,184] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:08,186] [INFO] DFAST_QC result json was written to GCF_000749865.1_ASM74986v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:08,186] [INFO] DFAST_QC completed!
[2024-01-25 17:40:08,187] [INFO] Total running time: 0h1m17s