[2024-01-24 13:36:45,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference
[2024-01-24 13:36:46,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,991] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg35484bf4-c7b9-418e-b1db-20207524e62b/GCF_014196515.1_ASM1419651v1_genomic.fna.gz | prodigal -d GCF_014196515.1_ASM1419651v1_genomic.fna/cds.fna -a GCF_014196515.1_ASM1419651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:02,859] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:02,859] [INFO] Task started: HMMsearch
[2024-01-24 13:37:02,859] [INFO] Running command: hmmsearch --tblout GCF_014196515.1_ASM1419651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference/reference_markers.hmm GCF_014196515.1_ASM1419651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:03,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:03,121] [INFO] Found 6/6 markers.
[2024-01-24 13:37:03,162] [INFO] Query marker FASTA was written to GCF_014196515.1_ASM1419651v1_genomic.fna/markers.fasta
[2024-01-24 13:37:03,162] [INFO] Task started: Blastn
[2024-01-24 13:37:03,163] [INFO] Running command: blastn -query GCF_014196515.1_ASM1419651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference/reference_markers.fasta -out GCF_014196515.1_ASM1419651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:03,985] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:03,988] [INFO] Selected 9 target genomes.
[2024-01-24 13:37:03,989] [INFO] Target genome list was writen to GCF_014196515.1_ASM1419651v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:03,993] [INFO] Task started: fastANI
[2024-01-24 13:37:03,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg35484bf4-c7b9-418e-b1db-20207524e62b/GCF_014196515.1_ASM1419651v1_genomic.fna.gz --refList GCF_014196515.1_ASM1419651v1_genomic.fna/target_genomes.txt --output GCF_014196515.1_ASM1419651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:14,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:14,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:14,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:14,925] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:14,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:14,926] [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
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	100.0	1581	1582	95	conclusive
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	99.9906	1571	1582	95	conclusive
Agrobacterium rubi	strain=NBRC 13261	GCA_000739935.1	28099	28099	type	True	85.0965	1194	1582	95	below_threshold
Agrobacterium rubi	strain=DSM 6772	GCA_017873055.1	28099	28099	type	True	85.0277	1193	1582	95	below_threshold
Agrobacterium rosae	strain=NCPPB 1650	GCA_002915175.1	1972867	1972867	type	True	83.6155	1032	1582	95	below_threshold
Agrobacterium bohemicum	strain=R90	GCA_002896715.1	2052828	2052828	type	True	83.0579	957	1582	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	78.078	404	1582	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.5894	330	1582	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	77.5148	385	1582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:14,928] [INFO] DFAST Taxonomy check result was written to GCF_014196515.1_ASM1419651v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:14,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:14,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:14,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference/checkm_data
[2024-01-24 13:37:14,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:14,975] [INFO] Task started: CheckM
[2024-01-24 13:37:14,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196515.1_ASM1419651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196515.1_ASM1419651v1_genomic.fna/checkm_input GCF_014196515.1_ASM1419651v1_genomic.fna/checkm_result
[2024-01-24 13:38:02,152] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:02,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:02,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:02,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:02,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196515.1_ASM1419651v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:02,170] [INFO] Task started: Blastn
[2024-01-24 13:38:02,170] [INFO] Running command: blastn -query GCF_014196515.1_ASM1419651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08aa6386-5fc9-4c3a-9e15-8425ceffff9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196515.1_ASM1419651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:03,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:03,733] [INFO] Selected 11 target genomes.
[2024-01-24 13:38:03,734] [INFO] Target genome list was writen to GCF_014196515.1_ASM1419651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:03,752] [INFO] Task started: fastANI
[2024-01-24 13:38:03,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg35484bf4-c7b9-418e-b1db-20207524e62b/GCF_014196515.1_ASM1419651v1_genomic.fna.gz --refList GCF_014196515.1_ASM1419651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196515.1_ASM1419651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:15,683] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:15,693] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:15,694] [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_014196515.1	s__Agrobacterium skierniewicense	100.0	1581	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	98.07	0.91	0.91	2	conclusive
GCF_000739935.1	s__Agrobacterium rubi	85.0895	1195	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.45	95.90	0.89	0.87	10	-
GCF_002915175.1	s__Agrobacterium rosae	83.6334	1030	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.78	95.28	0.91	0.82	8	-
GCA_900468015.1	s__Agrobacterium sp900468015	83.4451	940	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	95.47	95.47	0.86	0.86	2	-
GCA_900472925.1	s__Agrobacterium sp900472925	83.3815	988	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422245.1	s__Agrobacterium sp001422245	83.2661	926	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896715.1	s__Agrobacterium bohemicum	83.0562	958	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.81	99.81	1.00	1.00	2	-
GCF_000834635.1	s__Agrobacterium tumefaciens_C	82.5638	954	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.02	95.99	0.85	0.85	3	-
GCF_000949865.1	s__Agrobacterium nepotum	79.9124	675	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900012615.1	s__Agrobacterium sp900012615	79.8478	690	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	79.7316	684	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:15,696] [INFO] GTDB search result was written to GCF_014196515.1_ASM1419651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:15,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:15,702] [INFO] DFAST_QC result json was written to GCF_014196515.1_ASM1419651v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:15,703] [INFO] DFAST_QC completed!
[2024-01-24 13:38:15,703] [INFO] Total running time: 0h1m30s