[2024-01-25 18:58:05,827] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference
[2024-01-25 18:58:06,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:06,920] [INFO] Task started: Prodigal
[2024-01-25 18:58:06,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgcaa50865-1773-4c77-bdc6-f39644e25520/GCF_014639435.1_ASM1463943v1_genomic.fna.gz | prodigal -d GCF_014639435.1_ASM1463943v1_genomic.fna/cds.fna -a GCF_014639435.1_ASM1463943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:18,532] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:18,532] [INFO] Task started: HMMsearch
[2024-01-25 18:58:18,532] [INFO] Running command: hmmsearch --tblout GCF_014639435.1_ASM1463943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference/reference_markers.hmm GCF_014639435.1_ASM1463943v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:18,818] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:18,820] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcaa50865-1773-4c77-bdc6-f39644e25520/GCF_014639435.1_ASM1463943v1_genomic.fna.gz]
[2024-01-25 18:58:18,857] [INFO] Query marker FASTA was written to GCF_014639435.1_ASM1463943v1_genomic.fna/markers.fasta
[2024-01-25 18:58:18,857] [INFO] Task started: Blastn
[2024-01-25 18:58:18,857] [INFO] Running command: blastn -query GCF_014639435.1_ASM1463943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference/reference_markers.fasta -out GCF_014639435.1_ASM1463943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:19,570] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:19,573] [INFO] Selected 23 target genomes.
[2024-01-25 18:58:19,574] [INFO] Target genome list was writen to GCF_014639435.1_ASM1463943v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:19,585] [INFO] Task started: fastANI
[2024-01-25 18:58:19,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaa50865-1773-4c77-bdc6-f39644e25520/GCF_014639435.1_ASM1463943v1_genomic.fna.gz --refList GCF_014639435.1_ASM1463943v1_genomic.fna/target_genomes.txt --output GCF_014639435.1_ASM1463943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:39,616] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:39,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:39,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:39,628] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:58:39,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:58:39,628] [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
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	82.0608	865	1538	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	81.9471	861	1538	95	below_threshold
Ewingella americana	strain=CCUG 14506T	GCA_008693045.1	41202	41202	type	True	81.8088	858	1538	95	below_threshold
Ewingella americana	strain=NCTC12157	GCA_900451015.1	41202	41202	type	True	81.7802	867	1538	95	below_threshold
Ewingella americana	strain=ATCC 33852	GCA_000735345.1	41202	41202	type	True	81.7489	857	1538	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	81.721	884	1538	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	81.6299	840	1538	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	81.5322	842	1538	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	81.4587	844	1538	95	below_threshold
Rahnella aquatilis	strain=CIP 78.65	GCA_000241955.1	34038	34038	suspected-type	True	81.4562	881	1538	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	81.4117	865	1538	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	81.4039	830	1538	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	81.2818	857	1538	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	81.265	785	1538	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.5612	448	1538	95	below_threshold
Pectobacterium wasabiae	strain=NCPPB 3701	GCA_000749865.1	55208	55208	type	True	78.3606	285	1538	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	78.3437	287	1538	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	78.3291	290	1538	95	below_threshold
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	77.2779	126	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:39,630] [INFO] DFAST Taxonomy check result was written to GCF_014639435.1_ASM1463943v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:39,631] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:39,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:39,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference/checkm_data
[2024-01-25 18:58:39,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:39,676] [INFO] Task started: CheckM
[2024-01-25 18:58:39,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639435.1_ASM1463943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639435.1_ASM1463943v1_genomic.fna/checkm_input GCF_014639435.1_ASM1463943v1_genomic.fna/checkm_result
[2024-01-25 18:59:16,943] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:16,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:16,977] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:16,978] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:16,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639435.1_ASM1463943v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:16,978] [INFO] Task started: Blastn
[2024-01-25 18:59:16,978] [INFO] Running command: blastn -query GCF_014639435.1_ASM1463943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4746f2fc-23b9-4d51-acfb-16906f97c338/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639435.1_ASM1463943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:18,005] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:18,008] [INFO] Selected 20 target genomes.
[2024-01-25 18:59:18,008] [INFO] Target genome list was writen to GCF_014639435.1_ASM1463943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:18,031] [INFO] Task started: fastANI
[2024-01-25 18:59:18,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaa50865-1773-4c77-bdc6-f39644e25520/GCF_014639435.1_ASM1463943v1_genomic.fna.gz --refList GCF_014639435.1_ASM1463943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639435.1_ASM1463943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:37,538] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:37,550] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:37,550] [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_014639435.1	s__Ewingella psychrotolerans	100.0	1538	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006438725.1	s__Ewingella americana_A	85.1935	1132	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003864575.1	s__Ewingella sp003864575	84.4556	869	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013457415.1	s__Rahnella sp013457415	81.9937	858	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003263515.1	s__Rahnella inusitata	81.9385	862	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	-
GCF_000735345.1	s__Ewingella americana	81.7383	859	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	98.48	96.44	0.97	0.94	5	-
GCF_004330295.1	s__Rahnella victoriana	81.6152	841	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_002951615.1	s__Rahnella sp002951615	81.5674	835	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834385.1	s__Rahnella sp002834385	81.4133	830	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049675.1	s__Rahnella sp019049675	81.4059	830	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586165.1	s__Hafnia proteus	79.3758	289	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	-
GCF_004124235.1	s__Yersinia hibernica	78.6925	340	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_000633355.1	s__Serratia_A sp000633355	78.5807	417	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001053095.1	s__Yersinia similis	78.5275	281	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.47	99.21	0.94	0.92	9	-
GCF_000743355.1	s__Chania sp000743355	78.3567	374	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_001742185.1	s__Pectobacterium wasabiae	78.3428	289	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	-
GCF_002847015.1	s__ATCC-39006 sp002847015	78.0542	274	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__ATCC-39006	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001187905.1	s__Pantoea sp001187905	77.8012	324	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_000770305.1	s__Erwinia oleae	77.7556	273	1538	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.06	98.06	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:37,551] [INFO] GTDB search result was written to GCF_014639435.1_ASM1463943v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:37,551] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:37,554] [INFO] DFAST_QC result json was written to GCF_014639435.1_ASM1463943v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:37,555] [INFO] DFAST_QC completed!
[2024-01-25 18:59:37,555] [INFO] Total running time: 0h1m32s