[2024-01-24 13:31:41,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:41,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:41,812] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference
[2024-01-24 13:31:43,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:43,079] [INFO] Task started: Prodigal
[2024-01-24 13:31:43,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b32cffc-a24e-4a89-9b88-40dcbab104dc/GCF_012427845.1_ASM1242784v1_genomic.fna.gz | prodigal -d GCF_012427845.1_ASM1242784v1_genomic.fna/cds.fna -a GCF_012427845.1_ASM1242784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,056] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,056] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,056] [INFO] Running command: hmmsearch --tblout GCF_012427845.1_ASM1242784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference/reference_markers.hmm GCF_012427845.1_ASM1242784v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,371] [INFO] Found 6/6 markers.
[2024-01-24 13:31:56,439] [INFO] Query marker FASTA was written to GCF_012427845.1_ASM1242784v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,440] [INFO] Task started: Blastn
[2024-01-24 13:31:56,440] [INFO] Running command: blastn -query GCF_012427845.1_ASM1242784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference/reference_markers.fasta -out GCF_012427845.1_ASM1242784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,285] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,289] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:57,290] [INFO] Target genome list was writen to GCF_012427845.1_ASM1242784v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,376] [INFO] Task started: fastANI
[2024-01-24 13:31:57,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b32cffc-a24e-4a89-9b88-40dcbab104dc/GCF_012427845.1_ASM1242784v1_genomic.fna.gz --refList GCF_012427845.1_ASM1242784v1_genomic.fna/target_genomes.txt --output GCF_012427845.1_ASM1242784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:14,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:14,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:14,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:14,536] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:14,536] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:14,536] [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 punjabense	strain=SS95	GCA_012427845.1	2108399	2108399	type	True	100.0	1597	1597	95	conclusive
Pectobacterium punjabense	strain=SS95	GCA_003028395.1	2108399	2108399	type	True	99.9676	1532	1597	95	conclusive
Pectobacterium polonicum	strain=DPMP315	GCA_005497185.1	2485124	2485124	type	True	94.2587	1375	1597	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_000757625.1	1905730	1905730	type	True	91.4577	1324	1597	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_001742145.1	1905730	1905730	type	True	91.4297	1341	1597	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	91.1312	1309	1597	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	91.1219	1326	1597	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	89.0425	1211	1597	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.2249	1297	1597	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.975	388	1597	95	below_threshold
Cedecea davisae	strain=NCTC13724	GCA_900446735.1	158484	158484	type	True	78.952	302	1597	95	below_threshold
Enterobacter cancerogenus	strain=FDAARGOS 1428	GCA_019047785.1	69218	69218	type	True	78.647	322	1597	95	below_threshold
Cedecea davisae	strain=DSM 4568	GCA_000412335.2	158484	158484	type	True	78.4842	289	1597	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.4742	398	1597	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.4324	342	1597	95	below_threshold
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	78.0853	323	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:14,538] [INFO] DFAST Taxonomy check result was written to GCF_012427845.1_ASM1242784v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:14,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:14,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:14,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference/checkm_data
[2024-01-24 13:32:14,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:14,589] [INFO] Task started: CheckM
[2024-01-24 13:32:14,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012427845.1_ASM1242784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012427845.1_ASM1242784v1_genomic.fna/checkm_input GCF_012427845.1_ASM1242784v1_genomic.fna/checkm_result
[2024-01-24 13:32:57,038] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:57,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:57,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:57,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012427845.1_ASM1242784v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:57,064] [INFO] Task started: Blastn
[2024-01-24 13:32:57,065] [INFO] Running command: blastn -query GCF_012427845.1_ASM1242784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb76e73b-faa6-42ba-ab69-360672dbe84d/dqc_reference/reference_markers_gtdb.fasta -out GCF_012427845.1_ASM1242784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:58,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:58,177] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:58,177] [INFO] Target genome list was writen to GCF_012427845.1_ASM1242784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:58,235] [INFO] Task started: fastANI
[2024-01-24 13:32:58,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b32cffc-a24e-4a89-9b88-40dcbab104dc/GCF_012427845.1_ASM1242784v1_genomic.fna.gz --refList GCF_012427845.1_ASM1242784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012427845.1_ASM1242784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:12,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:12,075] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:12,076] [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_012427845.1	s__Pectobacterium punjabense	100.0	1597	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	conclusive
GCF_005497185.1	s__Pectobacterium polonicum	94.2587	1375	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742145.1	s__Pectobacterium parmentieri	91.4278	1341	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.20	98.87	0.95	0.90	33	-
GCF_001742185.1	s__Pectobacterium wasabiae	91.1211	1325	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	-
GCF_002847345.1	s__Pectobacterium peruviense	89.8391	1301	1597	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	89.6167	1304	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	-
GCF_000754695.1	s__Pectobacterium brasiliense	89.2963	1311	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_004137795.1	s__Pectobacterium zantedeschiae	89.2849	1313	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	-
GCF_000749845.1	s__Pectobacterium betavasculorum	88.9726	1193	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
GCF_019047785.1	s__Enterobacter cancerogenus	78.6303	323	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	-
GCF_000412335.2	s__Cedecea davisae	78.4567	291	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	98.19	96.20	0.94	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,077] [INFO] GTDB search result was written to GCF_012427845.1_ASM1242784v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:12,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:12,081] [INFO] DFAST_QC result json was written to GCF_012427845.1_ASM1242784v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:12,081] [INFO] DFAST_QC completed!
[2024-01-24 13:33:12,081] [INFO] Total running time: 0h1m30s