[2024-01-25 20:27:20,577] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference
[2024-01-25 20:27:21,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,824] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,824] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfa6e599-1cc7-4ee1-8aa9-930d96b486ec/GCF_002980495.1_ASM298049v1_genomic.fna.gz | prodigal -d GCF_002980495.1_ASM298049v1_genomic.fna/cds.fna -a GCF_002980495.1_ASM298049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:38,896] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:38,896] [INFO] Task started: HMMsearch
[2024-01-25 20:27:38,896] [INFO] Running command: hmmsearch --tblout GCF_002980495.1_ASM298049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference/reference_markers.hmm GCF_002980495.1_ASM298049v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:39,199] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:39,202] [INFO] Found 6/6 markers.
[2024-01-25 20:27:39,250] [INFO] Query marker FASTA was written to GCF_002980495.1_ASM298049v1_genomic.fna/markers.fasta
[2024-01-25 20:27:39,251] [INFO] Task started: Blastn
[2024-01-25 20:27:39,251] [INFO] Running command: blastn -query GCF_002980495.1_ASM298049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference/reference_markers.fasta -out GCF_002980495.1_ASM298049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:40,141] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:40,144] [INFO] Selected 22 target genomes.
[2024-01-25 20:27:40,145] [INFO] Target genome list was writen to GCF_002980495.1_ASM298049v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:40,189] [INFO] Task started: fastANI
[2024-01-25 20:27:40,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa6e599-1cc7-4ee1-8aa9-930d96b486ec/GCF_002980495.1_ASM298049v1_genomic.fna.gz --refList GCF_002980495.1_ASM298049v1_genomic.fna/target_genomes.txt --output GCF_002980495.1_ASM298049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:02,983] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:02,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:02,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:02,997] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:02,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:02,997] [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 phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	100.0	1832	1835	95	conclusive
Phyllobacterium salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	86.0628	1124	1835	95	below_threshold
Phyllobacterium leguminum	strain=ORS 1419	GCA_003217235.1	314237	314237	type	True	82.969	799	1835	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	79.0902	522	1835	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	78.4828	424	1835	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	78.4539	548	1835	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	78.4236	546	1835	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.4066	525	1835	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	78.3817	527	1835	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.3339	519	1835	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.3234	446	1835	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.3142	505	1835	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	78.2324	510	1835	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	78.2054	407	1835	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	78.2031	541	1835	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	77.9683	458	1835	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.8155	394	1835	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.246	259	1835	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.1559	270	1835	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.005	201	1835	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	76.8453	220	1835	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	76.8453	220	1835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:02,998] [INFO] DFAST Taxonomy check result was written to GCF_002980495.1_ASM298049v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:02,999] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:02,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:02,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference/checkm_data
[2024-01-25 20:28:03,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:03,050] [INFO] Task started: CheckM
[2024-01-25 20:28:03,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002980495.1_ASM298049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002980495.1_ASM298049v1_genomic.fna/checkm_input GCF_002980495.1_ASM298049v1_genomic.fna/checkm_result
[2024-01-25 20:28:53,437] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:53,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:53,468] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:53,468] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:53,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002980495.1_ASM298049v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:53,469] [INFO] Task started: Blastn
[2024-01-25 20:28:53,469] [INFO] Running command: blastn -query GCF_002980495.1_ASM298049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bae3b1a-4b77-4283-9c72-242f33d94b64/dqc_reference/reference_markers_gtdb.fasta -out GCF_002980495.1_ASM298049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:55,117] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:55,120] [INFO] Selected 10 target genomes.
[2024-01-25 20:28:55,120] [INFO] Target genome list was writen to GCF_002980495.1_ASM298049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:55,145] [INFO] Task started: fastANI
[2024-01-25 20:28:55,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa6e599-1cc7-4ee1-8aa9-930d96b486ec/GCF_002980495.1_ASM298049v1_genomic.fna.gz --refList GCF_002980495.1_ASM298049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002980495.1_ASM298049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:29:07,279] [INFO] Task succeeded: fastANI
[2024-01-25 20:29:07,311] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:29:07,311] [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_002980495.1	s__Paramesorhizobium phragmitis	100.0	1832	1835	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_003335045.1	s__Paramesorhizobium salinisoli	86.0627	1124	1835	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	85.017	1206	1835	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	84.845	1144	1835	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	82.9774	798	1835	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	81.8509	848	1835	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_006442815.1	s__Mesorhizobium sp006442815	78.4559	525	1835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_006440675.1	s__Mesorhizobium sp006440675	78.3983	523	1835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.39	95.73	0.91	0.84	9	-
GCA_017644005.1	s__RCIO01 sp017644005	77.6738	259	1835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	77.1371	273	1835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:29:07,313] [INFO] GTDB search result was written to GCF_002980495.1_ASM298049v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:29:07,314] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:29:07,318] [INFO] DFAST_QC result json was written to GCF_002980495.1_ASM298049v1_genomic.fna/dqc_result.json
[2024-01-25 20:29:07,318] [INFO] DFAST_QC completed!
[2024-01-25 20:29:07,318] [INFO] Total running time: 0h1m47s