[2024-01-24 11:20:34,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,053] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference
[2024-01-24 11:20:35,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,234] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,234] [INFO] Running command: gunzip -c /var/lib/cwl/stgc84f9e01-18d6-4259-be44-ad3ba272736b/GCF_014855505.1_ASM1485550v1_genomic.fna.gz | prodigal -d GCF_014855505.1_ASM1485550v1_genomic.fna/cds.fna -a GCF_014855505.1_ASM1485550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:47,686] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:47,687] [INFO] Task started: HMMsearch
[2024-01-24 11:20:47,687] [INFO] Running command: hmmsearch --tblout GCF_014855505.1_ASM1485550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference/reference_markers.hmm GCF_014855505.1_ASM1485550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:47,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:47,954] [INFO] Found 6/6 markers.
[2024-01-24 11:20:47,990] [INFO] Query marker FASTA was written to GCF_014855505.1_ASM1485550v1_genomic.fna/markers.fasta
[2024-01-24 11:20:47,991] [INFO] Task started: Blastn
[2024-01-24 11:20:47,991] [INFO] Running command: blastn -query GCF_014855505.1_ASM1485550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference/reference_markers.fasta -out GCF_014855505.1_ASM1485550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:48,743] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:48,747] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:48,748] [INFO] Target genome list was writen to GCF_014855505.1_ASM1485550v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:48,755] [INFO] Task started: fastANI
[2024-01-24 11:20:48,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgc84f9e01-18d6-4259-be44-ad3ba272736b/GCF_014855505.1_ASM1485550v1_genomic.fna.gz --refList GCF_014855505.1_ASM1485550v1_genomic.fna/target_genomes.txt --output GCF_014855505.1_ASM1485550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:04,087] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:04,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:04,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:04,103] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:21:04,103] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:21:04,103] [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
Musicola keenii	strain=A3967	GCA_014855505.1	2884250	2884250	type	True	100.0	1435	1438	95	inconclusive
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	100.0	1435	1438	95	inconclusive
Musicola paradisiaca	strain=NCPPB 2511	GCA_000400505.1	69223	69223	type	True	96.0904	1328	1438	95	inconclusive
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	81.263	884	1438	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	81.2599	899	1438	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	81.1531	863	1438	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	81.0557	879	1438	95	below_threshold
Dickeya undicola	strain=2B12	GCA_000784735.1	1577887	1577887	type	True	80.821	786	1438	95	below_threshold
Dickeya chrysanthemi	strain=NCPPB 402	GCA_000406105.1	556	556	type	True	80.7589	817	1438	95	below_threshold
Dickeya zeae	strain=NCPPB 2538	GCA_000406165.1	204042	204042	type	True	80.5422	749	1438	95	below_threshold
Dickeya parazeae	strain=S31	GCA_017897605.1	2893572	2893572	type	True	80.5341	760	1438	95	below_threshold
Dickeya oryzae	strain=ZYY5	GCA_009372235.1	1240404	1240404	type	True	80.3093	745	1438	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.8204	474	1438	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.3966	444	1438	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.2229	433	1438	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.0474	290	1438	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	77.8206	326	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:04,104] [INFO] DFAST Taxonomy check result was written to GCF_014855505.1_ASM1485550v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:04,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:04,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:04,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference/checkm_data
[2024-01-24 11:21:04,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:04,146] [INFO] Task started: CheckM
[2024-01-24 11:21:04,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014855505.1_ASM1485550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014855505.1_ASM1485550v1_genomic.fna/checkm_input GCF_014855505.1_ASM1485550v1_genomic.fna/checkm_result
[2024-01-24 11:21:43,111] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:43,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:43,129] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:43,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:43,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014855505.1_ASM1485550v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:43,130] [INFO] Task started: Blastn
[2024-01-24 11:21:43,130] [INFO] Running command: blastn -query GCF_014855505.1_ASM1485550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8b335f4-8513-4011-8b30-3a75c6dac53a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014855505.1_ASM1485550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:44,271] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:44,275] [INFO] Selected 15 target genomes.
[2024-01-24 11:21:44,275] [INFO] Target genome list was writen to GCF_014855505.1_ASM1485550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:44,288] [INFO] Task started: fastANI
[2024-01-24 11:21:44,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgc84f9e01-18d6-4259-be44-ad3ba272736b/GCF_014855505.1_ASM1485550v1_genomic.fna.gz --refList GCF_014855505.1_ASM1485550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014855505.1_ASM1485550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:56,703] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:56,718] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:56,718] [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_000400505.1	s__Dickeya paradisiaca	96.0904	1328	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.04	96.10	0.96	0.92	3	conclusive
GCF_002812485.1	s__Dickeya fangzhongdai	81.2573	901	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCF_001644705.1	s__Dickeya solani	81.071	879	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.95	98.75	1.00	0.95	38	-
GCF_000365305.1	s__Dickeya dianthicola	81.0394	839	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.46	97.48	0.95	0.91	50	-
GCF_000406145.1	s__Dickeya dadantii	81.0124	857	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	-
GCF_000784735.1	s__Dickeya undicola	80.8254	786	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.06	99.05	0.94	0.93	3	-
GCF_000406105.1	s__Dickeya chrysanthemi	80.7589	817	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
GCF_007858975.2	s__Dickeya poaceiphila	80.6287	728	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.40	98.88	0.98	0.96	3	-
GCF_000406165.1	s__Dickeya zeae	80.5348	750	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.51	96.16	0.94	0.92	9	-
GCF_009372235.1	s__Dickeya oryzae	80.3068	746	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.59	96.04	0.90	0.83	10	-
GCF_002291445.1	s__Brenneria goodwinii	78.6678	511	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:56,720] [INFO] GTDB search result was written to GCF_014855505.1_ASM1485550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:56,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:56,723] [INFO] DFAST_QC result json was written to GCF_014855505.1_ASM1485550v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:56,724] [INFO] DFAST_QC completed!
[2024-01-24 11:21:56,724] [INFO] Total running time: 0h1m23s