[2024-01-24 13:17:47,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:47,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:47,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference
[2024-01-24 13:17:48,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:48,759] [INFO] Task started: Prodigal
[2024-01-24 13:17:48,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgb01bf1b6-2486-47df-a670-b215d171a0d5/GCF_009498475.1_ASM949847v1_genomic.fna.gz | prodigal -d GCF_009498475.1_ASM949847v1_genomic.fna/cds.fna -a GCF_009498475.1_ASM949847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:07,258] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:07,259] [INFO] Task started: HMMsearch
[2024-01-24 13:18:07,259] [INFO] Running command: hmmsearch --tblout GCF_009498475.1_ASM949847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference/reference_markers.hmm GCF_009498475.1_ASM949847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:07,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:07,681] [INFO] Found 6/6 markers.
[2024-01-24 13:18:07,732] [INFO] Query marker FASTA was written to GCF_009498475.1_ASM949847v1_genomic.fna/markers.fasta
[2024-01-24 13:18:07,732] [INFO] Task started: Blastn
[2024-01-24 13:18:07,732] [INFO] Running command: blastn -query GCF_009498475.1_ASM949847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference/reference_markers.fasta -out GCF_009498475.1_ASM949847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,880] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,884] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:08,885] [INFO] Target genome list was writen to GCF_009498475.1_ASM949847v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:08,889] [INFO] Task started: fastANI
[2024-01-24 13:18:08,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01bf1b6-2486-47df-a670-b215d171a0d5/GCF_009498475.1_ASM949847v1_genomic.fna.gz --refList GCF_009498475.1_ASM949847v1_genomic.fna/target_genomes.txt --output GCF_009498475.1_ASM949847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:23,078] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:23,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:23,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:23,094] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:23,094] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:23,095] [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
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	100.0	1918	1919	95	conclusive
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	99.9855	1918	1919	95	conclusive
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	99.9649	1850	1919	95	conclusive
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	92.1478	1472	1919	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	90.6731	1385	1919	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	88.8859	1405	1919	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	88.3819	1418	1919	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.5795	606	1919	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.0295	717	1919	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.9329	544	1919	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:23,097] [INFO] DFAST Taxonomy check result was written to GCF_009498475.1_ASM949847v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:23,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:23,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:23,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference/checkm_data
[2024-01-24 13:18:23,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:23,155] [INFO] Task started: CheckM
[2024-01-24 13:18:23,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009498475.1_ASM949847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009498475.1_ASM949847v1_genomic.fna/checkm_input GCF_009498475.1_ASM949847v1_genomic.fna/checkm_result
[2024-01-24 13:19:17,374] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:17,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:17,396] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:17,397] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:17,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009498475.1_ASM949847v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:17,397] [INFO] Task started: Blastn
[2024-01-24 13:19:17,398] [INFO] Running command: blastn -query GCF_009498475.1_ASM949847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg274d828b-ea97-49df-bb52-33706f70e122/dqc_reference/reference_markers_gtdb.fasta -out GCF_009498475.1_ASM949847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:19,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:19,572] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:19,573] [INFO] Target genome list was writen to GCF_009498475.1_ASM949847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:19,590] [INFO] Task started: fastANI
[2024-01-24 13:19:19,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01bf1b6-2486-47df-a670-b215d171a0d5/GCF_009498475.1_ASM949847v1_genomic.fna.gz --refList GCF_009498475.1_ASM949847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009498475.1_ASM949847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:39,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:40,003] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:40,004] [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_001541315.1	s__Agrobacterium tumefaciens	99.9649	1850	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	conclusive
GCF_002943835.1	s__Agrobacterium deltaense	91.9197	1567	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	-
GCF_002008225.1	s__Agrobacterium salinitolerans	90.6731	1385	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	-
GCA_003241215.1	s__Agrobacterium fabrum_A	90.5744	1019	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	90.0067	1397	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	89.6605	1447	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_005221325.1	s__Agrobacterium sp900012625	89.5097	1503	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.19	97.65	0.98	0.95	4	-
GCF_900012615.1	s__Agrobacterium sp900012615	89.4883	1397	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCF_000092025.1	s__Agrobacterium fabrum	89.113	1480	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.52	95.41	0.93	0.85	28	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	88.8925	1434	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669145.1	s__Agrobacterium oryzihabitans	88.8891	1405	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCA_000949895.1	s__Agrobacterium arsenijevicii	88.4861	1409	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102105.1	s__Agrobacterium pusense	88.3722	1419	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.39	97.95	0.91	0.74	79	-
GCF_009649785.1	s__Agrobacterium fabacearum	87.8082	1420	1919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.40	96.96	0.89	0.76	243	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:40,009] [INFO] GTDB search result was written to GCF_009498475.1_ASM949847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:40,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:40,014] [INFO] DFAST_QC result json was written to GCF_009498475.1_ASM949847v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:40,014] [INFO] DFAST_QC completed!
[2024-01-24 13:19:40,015] [INFO] Total running time: 0h1m53s