[2024-01-24 11:26:28,187] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference
[2024-01-24 11:26:29,733] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,733] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,734] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe5e389b-4142-43dd-9f0a-fec1b1b3cac0/GCF_003335045.1_ASM333504v1_genomic.fna.gz | prodigal -d GCF_003335045.1_ASM333504v1_genomic.fna/cds.fna -a GCF_003335045.1_ASM333504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:44,814] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:44,815] [INFO] Task started: HMMsearch
[2024-01-24 11:26:44,815] [INFO] Running command: hmmsearch --tblout GCF_003335045.1_ASM333504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference/reference_markers.hmm GCF_003335045.1_ASM333504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:45,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:45,177] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,229] [INFO] Query marker FASTA was written to GCF_003335045.1_ASM333504v1_genomic.fna/markers.fasta
[2024-01-24 11:26:45,230] [INFO] Task started: Blastn
[2024-01-24 11:26:45,230] [INFO] Running command: blastn -query GCF_003335045.1_ASM333504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference/reference_markers.fasta -out GCF_003335045.1_ASM333504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,217] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,221] [INFO] Selected 15 target genomes.
[2024-01-24 11:26:46,221] [INFO] Target genome list was writen to GCF_003335045.1_ASM333504v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,224] [INFO] Task started: fastANI
[2024-01-24 11:26:46,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe5e389b-4142-43dd-9f0a-fec1b1b3cac0/GCF_003335045.1_ASM333504v1_genomic.fna.gz --refList GCF_003335045.1_ASM333504v1_genomic.fna/target_genomes.txt --output GCF_003335045.1_ASM333504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:03,234] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:03,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:03,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:03,249] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:03,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:03,250] [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 salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	100.0	1622	1624	95	conclusive
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	86.0977	1111	1624	95	below_threshold
Phyllobacterium leguminum	strain=ORS 1419	GCA_003217235.1	314237	314237	type	True	82.8051	808	1624	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	78.5549	507	1624	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	78.3526	506	1624	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.3284	426	1624	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	78.316	512	1624	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.3074	478	1624	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	78.1896	457	1624	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.1056	479	1624	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	78.0964	507	1624	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	78.0627	474	1624	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	78.0386	478	1624	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.934	361	1624	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.9189	355	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:03,252] [INFO] DFAST Taxonomy check result was written to GCF_003335045.1_ASM333504v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:03,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:03,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:03,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference/checkm_data
[2024-01-24 11:27:03,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:03,307] [INFO] Task started: CheckM
[2024-01-24 11:27:03,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003335045.1_ASM333504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003335045.1_ASM333504v1_genomic.fna/checkm_input GCF_003335045.1_ASM333504v1_genomic.fna/checkm_result
[2024-01-24 11:27:48,742] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:48,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:48,765] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:48,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:48,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003335045.1_ASM333504v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:48,766] [INFO] Task started: Blastn
[2024-01-24 11:27:48,766] [INFO] Running command: blastn -query GCF_003335045.1_ASM333504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50a9484e-ec36-43c2-8579-1761b3c350ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_003335045.1_ASM333504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:50,664] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:50,668] [INFO] Selected 6 target genomes.
[2024-01-24 11:27:50,668] [INFO] Target genome list was writen to GCF_003335045.1_ASM333504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:50,669] [INFO] Task started: fastANI
[2024-01-24 11:27:50,670] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe5e389b-4142-43dd-9f0a-fec1b1b3cac0/GCF_003335045.1_ASM333504v1_genomic.fna.gz --refList GCF_003335045.1_ASM333504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003335045.1_ASM333504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:57,974] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:57,983] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:57,984] [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_003335045.1	s__Paramesorhizobium salinisoli	100.0	1622	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002980495.1	s__Paramesorhizobium phragmitis	86.1183	1109	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	84.2835	1109	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558695.1	s__Paramesorhizobium deserti	84.1521	1130	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217235.1	s__Paramesorhizobium leguminum	82.7834	810	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640615.1	s__Paramesorhizobium endophyticum	81.5275	849	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:57,985] [INFO] GTDB search result was written to GCF_003335045.1_ASM333504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:57,986] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:57,989] [INFO] DFAST_QC result json was written to GCF_003335045.1_ASM333504v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:57,989] [INFO] DFAST_QC completed!
[2024-01-24 11:27:57,989] [INFO] Total running time: 0h1m30s