[2024-01-24 13:13:51,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference
[2024-01-24 13:13:52,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,713] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,713] [INFO] Running command: gunzip -c /var/lib/cwl/stga1e990e3-26af-41bd-be72-0896a075399a/GCF_006094455.1_ASM609445v1_genomic.fna.gz | prodigal -d GCF_006094455.1_ASM609445v1_genomic.fna/cds.fna -a GCF_006094455.1_ASM609445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:02,616] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:02,616] [INFO] Task started: HMMsearch
[2024-01-24 13:14:02,616] [INFO] Running command: hmmsearch --tblout GCF_006094455.1_ASM609445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference/reference_markers.hmm GCF_006094455.1_ASM609445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:02,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:02,994] [INFO] Found 6/6 markers.
[2024-01-24 13:14:03,027] [INFO] Query marker FASTA was written to GCF_006094455.1_ASM609445v1_genomic.fna/markers.fasta
[2024-01-24 13:14:03,027] [INFO] Task started: Blastn
[2024-01-24 13:14:03,027] [INFO] Running command: blastn -query GCF_006094455.1_ASM609445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference/reference_markers.fasta -out GCF_006094455.1_ASM609445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:03,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:03,995] [INFO] Selected 16 target genomes.
[2024-01-24 13:14:03,996] [INFO] Target genome list was writen to GCF_006094455.1_ASM609445v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:04,007] [INFO] Task started: fastANI
[2024-01-24 13:14:04,008] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e990e3-26af-41bd-be72-0896a075399a/GCF_006094455.1_ASM609445v1_genomic.fna.gz --refList GCF_006094455.1_ASM609445v1_genomic.fna/target_genomes.txt --output GCF_006094455.1_ASM609445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:18,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:18,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:18,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:18,501] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:14:18,501] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:18,502] [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
Morganella morganii subsp. morganii	strain=ATCC 25830	GCA_006094455.1	180434	582	type	True	100.0	1295	1296	95	conclusive
Morganella morganii	strain=DSM 30164	GCA_019243775.1	582	582	type	True	98.8266	1207	1296	95	conclusive
Morganella morganii subsp. morganii	strain=NBRC 3848	GCA_001598895.1	180434	582	type	True	98.8032	1196	1296	95	conclusive
Morganella psychrotolerans	strain=GCSL-P101	GCA_001676155.1	368603	368603	type	True	83.8596	972	1296	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.6094	235	1296	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	78.3822	242	1296	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.3559	237	1296	95	below_threshold
Xenorhabdus mauleonii	strain=DSM 17908	GCA_002632685.1	351675	351675	type	True	78.3	174	1296	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	78.2885	244	1296	95	below_threshold
Shimwellia blattae	strain=NBRC 105725	GCA_000327265.1	563	563	type	True	78.1237	267	1296	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	77.9953	250	1296	95	below_threshold
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	77.9491	253	1296	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.7194	265	1296	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	77.7033	217	1296	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	77.6166	241	1296	95	below_threshold
Rouxiella aceris	strain=SAP-1	GCA_012933545.1	2703884	2703884	type	True	77.5601	209	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,504] [INFO] DFAST Taxonomy check result was written to GCF_006094455.1_ASM609445v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:18,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:18,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:18,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference/checkm_data
[2024-01-24 13:14:18,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:18,551] [INFO] Task started: CheckM
[2024-01-24 13:14:18,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006094455.1_ASM609445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006094455.1_ASM609445v1_genomic.fna/checkm_input GCF_006094455.1_ASM609445v1_genomic.fna/checkm_result
[2024-01-24 13:14:54,184] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:54,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:54,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:54,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:54,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006094455.1_ASM609445v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:54,216] [INFO] Task started: Blastn
[2024-01-24 13:14:54,216] [INFO] Running command: blastn -query GCF_006094455.1_ASM609445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec0a85e9-30c5-4670-9cd2-ac8146d15e96/dqc_reference/reference_markers_gtdb.fasta -out GCF_006094455.1_ASM609445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:55,338] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:55,349] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:55,349] [INFO] Target genome list was writen to GCF_006094455.1_ASM609445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:55,359] [INFO] Task started: fastANI
[2024-01-24 13:14:55,359] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e990e3-26af-41bd-be72-0896a075399a/GCF_006094455.1_ASM609445v1_genomic.fna.gz --refList GCF_006094455.1_ASM609445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006094455.1_ASM609445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:05,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:05,341] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:05,342] [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_019243775.1	s__Morganella morganii	98.8469	1206	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	98.34	95.47	0.94	0.88	171	conclusive
GCF_000633515.1	s__Morganella morganii_B	94.1215	1109	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	96.84	95.81	0.92	0.90	4	-
GCF_003996855.1	s__Morganella morganii_C	92.1093	1055	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019242955.1	s__Morganella morganii_A	92.0001	1143	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.48	97.24	0.94	0.90	21	-
GCF_001676055.1	s__Morganella psychrotolerans_B	83.9585	1011	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	95.92	95.92	0.88	0.88	2	-
GCF_001676155.1	s__Morganella psychrotolerans	83.8529	972	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.64	95.31	0.94	0.87	3	-
GCF_011046025.1	s__Proteus sp011046025	79.4544	151	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.836	N/A	N/A	N/A	N/A	1	-
GCF_017348915.1	s__UBA7405 sp000755535	78.6594	237	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
GCF_009363175.1	s__Citrobacter_A telavivensis	78.4206	265	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002953215.1	s__Mixta calida	78.398	234	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:05,344] [INFO] GTDB search result was written to GCF_006094455.1_ASM609445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:05,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:05,348] [INFO] DFAST_QC result json was written to GCF_006094455.1_ASM609445v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:05,348] [INFO] DFAST_QC completed!
[2024-01-24 13:15:05,348] [INFO] Total running time: 0h1m14s