[2024-01-24 15:17:48,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:48,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:48,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference
[2024-01-24 15:17:51,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,534] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg62fc35a0-8668-4fe8-a39a-1b9a32cbe333/GCF_003144395.1_ASM314439v1_genomic.fna.gz | prodigal -d GCF_003144395.1_ASM314439v1_genomic.fna/cds.fna -a GCF_003144395.1_ASM314439v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:17:59,253] [INFO] Task succeeded: Prodigal
[2024-01-24 15:17:59,253] [INFO] Task started: HMMsearch
[2024-01-24 15:17:59,254] [INFO] Running command: hmmsearch --tblout GCF_003144395.1_ASM314439v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference/reference_markers.hmm GCF_003144395.1_ASM314439v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:17:59,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:17:59,549] [INFO] Found 6/6 markers.
[2024-01-24 15:17:59,581] [INFO] Query marker FASTA was written to GCF_003144395.1_ASM314439v1_genomic.fna/markers.fasta
[2024-01-24 15:17:59,582] [INFO] Task started: Blastn
[2024-01-24 15:17:59,582] [INFO] Running command: blastn -query GCF_003144395.1_ASM314439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference/reference_markers.fasta -out GCF_003144395.1_ASM314439v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:00,702] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:00,710] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:00,710] [INFO] Target genome list was writen to GCF_003144395.1_ASM314439v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:00,724] [INFO] Task started: fastANI
[2024-01-24 15:18:00,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg62fc35a0-8668-4fe8-a39a-1b9a32cbe333/GCF_003144395.1_ASM314439v1_genomic.fna.gz --refList GCF_003144395.1_ASM314439v1_genomic.fna/target_genomes.txt --output GCF_003144395.1_ASM314439v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:12,759] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:12,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:12,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:12,774] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:12,775] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:12,775] [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 faecis	strain=TJ1636	GCA_003144395.1	2050967	2050967	type	True	100.0	1272	1275	95	conclusive
Proteus penneri	strain=ATCC 33519	GCA_003144535.1	102862	102862	type	True	93.8648	1132	1275	95	below_threshold
Proteus penneri	strain=NCTC12737	GCA_900455015.1	102862	102862	type	True	93.8502	1122	1275	95	below_threshold
Proteus penneri	strain=FDAARGOS_874	GCA_016028675.1	102862	102862	type	True	93.8406	1146	1275	95	below_threshold
Proteus cibi	strain=FJ2001126-3	GCA_003144405.1	2050966	2050966	type	True	93.0318	1123	1275	95	below_threshold
Proteus columbae	strain=08MAS2615	GCA_002777965.1	1987580	1987580	type	True	92.8705	1126	1275	95	below_threshold
Proteus alimentorum	strain=08MAS0041	GCA_002607735.1	1973495	1973495	type	True	92.6163	1088	1275	95	below_threshold
Proteus terrae subsp. cibarius	strain=JCM 30699	GCA_003144495.1	626774	1574161	type	True	91.9487	1107	1275	95	below_threshold
Proteus terrae	strain=LMG 28659	GCA_003144325.1	1574161	1574161	type	True	91.8636	1113	1275	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	78.819	78	1275	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.1078	173	1275	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	77.9348	112	1275	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.1847	90	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:12,776] [INFO] DFAST Taxonomy check result was written to GCF_003144395.1_ASM314439v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:12,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:12,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:12,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference/checkm_data
[2024-01-24 15:18:12,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:12,817] [INFO] Task started: CheckM
[2024-01-24 15:18:12,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003144395.1_ASM314439v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003144395.1_ASM314439v1_genomic.fna/checkm_input GCF_003144395.1_ASM314439v1_genomic.fna/checkm_result
[2024-01-24 15:18:42,392] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:42,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:42,419] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:42,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:42,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003144395.1_ASM314439v1_genomic.fna/markers.fasta)
[2024-01-24 15:18:42,421] [INFO] Task started: Blastn
[2024-01-24 15:18:42,421] [INFO] Running command: blastn -query GCF_003144395.1_ASM314439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86802e2d-0b20-4b00-8a71-af7bf2a9318a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003144395.1_ASM314439v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:43,486] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:43,493] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:43,494] [INFO] Target genome list was writen to GCF_003144395.1_ASM314439v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:43,505] [INFO] Task started: fastANI
[2024-01-24 15:18:43,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg62fc35a0-8668-4fe8-a39a-1b9a32cbe333/GCF_003144395.1_ASM314439v1_genomic.fna.gz --refList GCF_003144395.1_ASM314439v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003144395.1_ASM314439v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:18:54,235] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:54,250] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:18:54,250] [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_003144395.1	s__Proteus faecis	100.0	1272	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.18	98.84	0.96	0.95	3	conclusive
GCF_003144535.1	s__Proteus penneri	93.8498	1133	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.41	98.65	0.95	0.93	24	-
GCF_003144405.1	s__Proteus cibi	93.0318	1123	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.44	99.18	0.92	0.85	4	-
GCF_002777965.1	s__Proteus columbae	92.8705	1126	1275	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	92.6163	1088	1275	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	92.4741	1133	1275	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	92.1027	1114	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.5013	98.84	97.67	0.96	0.91	3	-
GCF_011046025.1	s__Proteus sp011046025	91.9726	1105	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.836	N/A	N/A	N/A	N/A	1	-
GCF_003144325.1	s__Proteus terrae	91.8636	1113	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.30	96.81	0.93	0.92	6	-
GCF_016239305.1	s__Proteus vulgaris_C	89.0894	1091	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901472505.1	s__Proteus vulgaris	89.0885	1109	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.65	99.53	0.96	0.94	17	-
--------------------------------------------------------------------------------
[2024-01-24 15:18:54,252] [INFO] GTDB search result was written to GCF_003144395.1_ASM314439v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:18:54,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:18:54,260] [INFO] DFAST_QC result json was written to GCF_003144395.1_ASM314439v1_genomic.fna/dqc_result.json
[2024-01-24 15:18:54,260] [INFO] DFAST_QC completed!
[2024-01-24 15:18:54,260] [INFO] Total running time: 0h1m5s