[2024-01-24 10:47:40,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference
[2024-01-24 10:47:44,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,788] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e63f338-6010-4ee9-9349-be663a166d0a/GCF_003144535.1_ASM314453v1_genomic.fna.gz | prodigal -d GCF_003144535.1_ASM314453v1_genomic.fna/cds.fna -a GCF_003144535.1_ASM314453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:52,270] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:52,271] [INFO] Task started: HMMsearch
[2024-01-24 10:47:52,271] [INFO] Running command: hmmsearch --tblout GCF_003144535.1_ASM314453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference/reference_markers.hmm GCF_003144535.1_ASM314453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:52,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:52,582] [INFO] Found 6/6 markers.
[2024-01-24 10:47:52,618] [INFO] Query marker FASTA was written to GCF_003144535.1_ASM314453v1_genomic.fna/markers.fasta
[2024-01-24 10:47:52,618] [INFO] Task started: Blastn
[2024-01-24 10:47:52,619] [INFO] Running command: blastn -query GCF_003144535.1_ASM314453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference/reference_markers.fasta -out GCF_003144535.1_ASM314453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:53,327] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:53,332] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:53,332] [INFO] Target genome list was writen to GCF_003144535.1_ASM314453v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:53,343] [INFO] Task started: fastANI
[2024-01-24 10:47:53,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e63f338-6010-4ee9-9349-be663a166d0a/GCF_003144535.1_ASM314453v1_genomic.fna.gz --refList GCF_003144535.1_ASM314453v1_genomic.fna/target_genomes.txt --output GCF_003144535.1_ASM314453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:04,950] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:04,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:04,963] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:48:04,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:04,963] [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
Proteus penneri	strain=ATCC 33519	GCA_003144535.1	102862	102862	type	True	100.0	1243	1244	95	conclusive
Proteus penneri	strain=FDAARGOS_874	GCA_016028675.1	102862	102862	type	True	99.9992	1243	1244	95	conclusive
Proteus penneri	strain=NCTC12737	GCA_900455015.1	102862	102862	type	True	99.5192	1192	1244	95	conclusive
Proteus faecis	strain=TJ1636	GCA_003144395.1	2050967	2050967	type	True	93.9445	1130	1244	95	below_threshold
Proteus columbae	strain=08MAS2615	GCA_002777965.1	1987580	1987580	type	True	92.2622	1114	1244	95	below_threshold
Proteus cibi	strain=FJ2001126-3	GCA_003144405.1	2050966	2050966	type	True	92.1961	1099	1244	95	below_threshold
Proteus alimentorum	strain=08MAS0041	GCA_002607735.1	1973495	1973495	type	True	92.1684	1074	1244	95	below_threshold
Proteus terrae	strain=LMG 28659	GCA_003144325.1	1574161	1574161	type	True	91.7662	1110	1244	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.1526	87	1244	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	77.871	110	1244	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	77.8338	191	1244	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	77.7465	100	1244	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	77.6438	203	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,966] [INFO] DFAST Taxonomy check result was written to GCF_003144535.1_ASM314453v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:04,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:04,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:04,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference/checkm_data
[2024-01-24 10:48:04,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:05,003] [INFO] Task started: CheckM
[2024-01-24 10:48:05,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003144535.1_ASM314453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003144535.1_ASM314453v1_genomic.fna/checkm_input GCF_003144535.1_ASM314453v1_genomic.fna/checkm_result
[2024-01-24 10:48:33,056] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:33,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:33,072] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:33,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:33,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003144535.1_ASM314453v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:33,073] [INFO] Task started: Blastn
[2024-01-24 10:48:33,074] [INFO] Running command: blastn -query GCF_003144535.1_ASM314453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg753137f7-58ab-4e9f-a02e-f08af92d1792/dqc_reference/reference_markers_gtdb.fasta -out GCF_003144535.1_ASM314453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:34,046] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:34,050] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:34,050] [INFO] Target genome list was writen to GCF_003144535.1_ASM314453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:34,068] [INFO] Task started: fastANI
[2024-01-24 10:48:34,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e63f338-6010-4ee9-9349-be663a166d0a/GCF_003144535.1_ASM314453v1_genomic.fna.gz --refList GCF_003144535.1_ASM314453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003144535.1_ASM314453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:46,942] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:46,957] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:46,957] [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_003144535.1	s__Proteus penneri	100.0	1243	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.41	98.65	0.95	0.93	24	conclusive
GCF_003144395.1	s__Proteus faecis	93.9275	1131	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.18	98.84	0.96	0.95	3	-
GCF_002777965.1	s__Proteus columbae	92.2574	1115	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144405.1	s__Proteus cibi	92.1961	1099	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.44	99.18	0.92	0.85	4	-
GCF_002607735.1	s__Proteus alimentorum	92.1847	1073	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	96.99	96.99	0.91	0.91	3	-
GCF_009914335.1	s__Proteus sp003144505	91.9844	1097	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.18	97.72	0.94	0.91	8	-
GCF_016647575.1	s__Proteus mirabilis_B	91.954	1086	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.5013	98.84	97.67	0.96	0.91	3	-
GCF_011045835.1	s__Proteus cibarius	91.788	1090	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.79	96.76	0.92	0.88	25	-
GCF_003144325.1	s__Proteus terrae	91.7744	1109	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.30	96.81	0.93	0.92	6	-
GCF_011046025.1	s__Proteus sp011046025	91.6875	1093	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.836	N/A	N/A	N/A	N/A	1	-
GCF_003144375.1	s__Proteus sp003144375	91.4571	1081	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.93	98.24	0.92	0.92	3	-
GCF_001722135.1	s__Proteus sp001722135	91.2012	1104	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_011045815.1	s__Proteus vulgaris_B	90.8311	1128	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.83	98.17	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,960] [INFO] GTDB search result was written to GCF_003144535.1_ASM314453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:46,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:46,964] [INFO] DFAST_QC result json was written to GCF_003144535.1_ASM314453v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:46,964] [INFO] DFAST_QC completed!
[2024-01-24 10:48:46,965] [INFO] Total running time: 0h1m6s