[2024-01-24 12:53:37,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference
[2024-01-24 12:53:38,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,530] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg326f3f5b-463f-4eb7-9ce2-b0777b159457/GCF_003010965.1_ASM301096v1_genomic.fna.gz | prodigal -d GCF_003010965.1_ASM301096v1_genomic.fna/cds.fna -a GCF_003010965.1_ASM301096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:58,190] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:58,191] [INFO] Task started: HMMsearch
[2024-01-24 12:53:58,191] [INFO] Running command: hmmsearch --tblout GCF_003010965.1_ASM301096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference/reference_markers.hmm GCF_003010965.1_ASM301096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:58,503] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:58,504] [INFO] Found 6/6 markers.
[2024-01-24 12:53:58,562] [INFO] Query marker FASTA was written to GCF_003010965.1_ASM301096v1_genomic.fna/markers.fasta
[2024-01-24 12:53:58,563] [INFO] Task started: Blastn
[2024-01-24 12:53:58,563] [INFO] Running command: blastn -query GCF_003010965.1_ASM301096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference/reference_markers.fasta -out GCF_003010965.1_ASM301096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:59,468] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:59,472] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:59,473] [INFO] Target genome list was writen to GCF_003010965.1_ASM301096v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:59,493] [INFO] Task started: fastANI
[2024-01-24 12:53:59,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg326f3f5b-463f-4eb7-9ce2-b0777b159457/GCF_003010965.1_ASM301096v1_genomic.fna.gz --refList GCF_003010965.1_ASM301096v1_genomic.fna/target_genomes.txt --output GCF_003010965.1_ASM301096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:16,309] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:16,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:16,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:16,327] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:16,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:16,328] [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
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	100.0	2095	2097	95	conclusive
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	86.1856	1349	2097	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	82.0924	1162	2097	95	below_threshold
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	80.9076	1032	2097	95	below_threshold
Phyllobacterium bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	80.8127	1018	2097	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	80.1667	859	2097	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	79.9766	823	2097	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	77.4085	229	2097	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	77.2693	358	2097	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	77.2159	333	2097	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	77.0736	367	2097	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	76.9921	154	2097	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.9532	253	2097	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.7735	220	2097	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	76.5869	225	2097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:16,329] [INFO] DFAST Taxonomy check result was written to GCF_003010965.1_ASM301096v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:16,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:16,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:16,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference/checkm_data
[2024-01-24 12:54:16,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:16,398] [INFO] Task started: CheckM
[2024-01-24 12:54:16,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003010965.1_ASM301096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003010965.1_ASM301096v1_genomic.fna/checkm_input GCF_003010965.1_ASM301096v1_genomic.fna/checkm_result
[2024-01-24 12:55:13,760] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:13,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:13,781] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:13,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:13,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003010965.1_ASM301096v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:13,782] [INFO] Task started: Blastn
[2024-01-24 12:55:13,783] [INFO] Running command: blastn -query GCF_003010965.1_ASM301096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9126058d-98fb-4d49-9142-edda7d7454a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003010965.1_ASM301096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:15,441] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:15,445] [INFO] Selected 11 target genomes.
[2024-01-24 12:55:15,445] [INFO] Target genome list was writen to GCF_003010965.1_ASM301096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:15,478] [INFO] Task started: fastANI
[2024-01-24 12:55:15,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg326f3f5b-463f-4eb7-9ce2-b0777b159457/GCF_003010965.1_ASM301096v1_genomic.fna.gz --refList GCF_003010965.1_ASM301096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003010965.1_ASM301096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:28,103] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:28,120] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:28,120] [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_003010965.1	s__Phyllobacterium sophorae	100.0	2095	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.00	98.48	0.92	0.90	3	conclusive
GCF_002764115.1	s__Phyllobacterium zundukense	86.1731	1351	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003010955.1	s__Phyllobacterium brassicacearum	82.0789	1164	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900473175.1	s__Phyllobacterium sp900473175	81.2463	1006	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192095.1	s__Phyllobacterium trifolii	80.922	1030	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.32	99.28	0.88	0.88	4	-
GCF_003337575.1	s__Phyllobacterium bourgognense	80.8136	1018	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833775.1	s__Phyllobacterium sp017833775	80.5086	908	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013327855.1	s__Phyllobacterium pellucidum	79.9638	825	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	97.81	96.22	0.94	0.90	6	-
GCA_900472835.1	s__Phyllobacterium sp900472835	79.5615	738	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.91	98.56	0.99	0.96	30	-
GCF_900104355.1	s__Phyllobacterium sp900104355	79.5294	763	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465915.1	s__63-22 sp900465915	77.2112	299	2097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	97.55	97.55	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:28,122] [INFO] GTDB search result was written to GCF_003010965.1_ASM301096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:28,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:28,126] [INFO] DFAST_QC result json was written to GCF_003010965.1_ASM301096v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:28,126] [INFO] DFAST_QC completed!
[2024-01-24 12:55:28,126] [INFO] Total running time: 0h1m51s