[2024-01-24 11:35:10,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference
[2024-01-24 11:35:12,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,131] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c8990ad-a8b8-49ea-b9db-52d9afed1ec2/GCF_003144495.1_ASM314449v1_genomic.fna.gz | prodigal -d GCF_003144495.1_ASM314449v1_genomic.fna/cds.fna -a GCF_003144495.1_ASM314449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:19,943] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:19,944] [INFO] Task started: HMMsearch
[2024-01-24 11:35:19,944] [INFO] Running command: hmmsearch --tblout GCF_003144495.1_ASM314449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference/reference_markers.hmm GCF_003144495.1_ASM314449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:20,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:20,253] [INFO] Found 6/6 markers.
[2024-01-24 11:35:20,286] [INFO] Query marker FASTA was written to GCF_003144495.1_ASM314449v1_genomic.fna/markers.fasta
[2024-01-24 11:35:20,286] [INFO] Task started: Blastn
[2024-01-24 11:35:20,287] [INFO] Running command: blastn -query GCF_003144495.1_ASM314449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference/reference_markers.fasta -out GCF_003144495.1_ASM314449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:21,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:21,043] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:21,044] [INFO] Target genome list was writen to GCF_003144495.1_ASM314449v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:21,050] [INFO] Task started: fastANI
[2024-01-24 11:35:21,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8990ad-a8b8-49ea-b9db-52d9afed1ec2/GCF_003144495.1_ASM314449v1_genomic.fna.gz --refList GCF_003144495.1_ASM314449v1_genomic.fna/target_genomes.txt --output GCF_003144495.1_ASM314449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:32,087] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:32,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:32,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:32,109] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:32,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:32,110] [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 terrae subsp. cibarius	strain=JCM 30699	GCA_003144495.1	626774	1574161	type	True	100.0	1281	1284	95	conclusive
Proteus terrae	strain=LMG 28659	GCA_003144325.1	1574161	1574161	type	True	96.5898	1174	1284	95	conclusive
Proteus columbae	strain=08MAS2615	GCA_002777965.1	1987580	1987580	type	True	92.8898	1148	1284	95	below_threshold
Proteus alimentorum	strain=08MAS0041	GCA_002607735.1	1973495	1973495	type	True	92.6932	1108	1284	95	below_threshold
Proteus cibi	strain=FJ2001126-3	GCA_003144405.1	2050966	2050966	type	True	92.237	1140	1284	95	below_threshold
Proteus faecis	strain=TJ1636	GCA_003144395.1	2050967	2050967	type	True	91.9815	1101	1284	95	below_threshold
Proteus penneri	strain=NCTC12737	GCA_900455015.1	102862	102862	type	True	91.7845	1109	1284	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	78.0939	275	1284	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	77.9407	195	1284	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	77.7185	97	1284	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	76.4806	87	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:32,115] [INFO] DFAST Taxonomy check result was written to GCF_003144495.1_ASM314449v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:32,116] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:32,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:32,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference/checkm_data
[2024-01-24 11:35:32,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:32,165] [INFO] Task started: CheckM
[2024-01-24 11:35:32,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003144495.1_ASM314449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003144495.1_ASM314449v1_genomic.fna/checkm_input GCF_003144495.1_ASM314449v1_genomic.fna/checkm_result
[2024-01-24 11:36:01,594] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:01,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,615] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:01,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:01,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003144495.1_ASM314449v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:01,617] [INFO] Task started: Blastn
[2024-01-24 11:36:01,617] [INFO] Running command: blastn -query GCF_003144495.1_ASM314449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1c978ad-2cad-4829-aee5-5753315f6115/dqc_reference/reference_markers_gtdb.fasta -out GCF_003144495.1_ASM314449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:02,589] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:02,593] [INFO] Selected 10 target genomes.
[2024-01-24 11:36:02,593] [INFO] Target genome list was writen to GCF_003144495.1_ASM314449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:02,600] [INFO] Task started: fastANI
[2024-01-24 11:36:02,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8990ad-a8b8-49ea-b9db-52d9afed1ec2/GCF_003144495.1_ASM314449v1_genomic.fna.gz --refList GCF_003144495.1_ASM314449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003144495.1_ASM314449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:12,021] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,034] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:36:12,035] [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_011045835.1	s__Proteus cibarius	98.9398	1176	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.79	96.76	0.92	0.88	25	inconclusive
GCF_003144325.1	s__Proteus terrae	96.5746	1175	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.30	96.81	0.93	0.92	6	inconclusive
GCF_011046025.1	s__Proteus sp011046025	95.2994	1158	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.836	N/A	N/A	N/A	N/A	1	-
GCF_016647575.1	s__Proteus mirabilis_B	95.1715	1170	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.5013	98.84	97.67	0.96	0.91	3	-
GCF_002777965.1	s__Proteus columbae	92.8872	1148	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002607735.1	s__Proteus alimentorum	92.6932	1108	1284	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	92.5521	1144	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.18	97.72	0.94	0.91	8	-
GCA_901472505.1	s__Proteus vulgaris	90.0665	1124	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.65	99.53	0.96	0.94	17	-
GCF_002812485.1	s__Dickeya fangzhongdai	78.0916	60	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCA_016618195.1	s__Providencia stuartii_A	78.0817	277	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.56	98.52	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,036] [INFO] GTDB search result was written to GCF_003144495.1_ASM314449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:12,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:12,040] [INFO] DFAST_QC result json was written to GCF_003144495.1_ASM314449v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:12,040] [INFO] DFAST_QC completed!
[2024-01-24 11:36:12,040] [INFO] Total running time: 0h1m1s