[2024-01-25 18:01:50,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:50,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:50,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference
[2024-01-25 18:01:51,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:51,753] [INFO] Task started: Prodigal
[2024-01-25 18:01:51,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg985db758-289c-45bd-934e-dc22631ae821/GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna.gz | prodigal -d GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/cds.fna -a GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:07,595] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:07,595] [INFO] Task started: HMMsearch
[2024-01-25 18:02:07,595] [INFO] Running command: hmmsearch --tblout GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference/reference_markers.hmm GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:07,958] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:07,959] [INFO] Found 6/6 markers.
[2024-01-25 18:02:08,006] [INFO] Query marker FASTA was written to GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/markers.fasta
[2024-01-25 18:02:08,006] [INFO] Task started: Blastn
[2024-01-25 18:02:08,006] [INFO] Running command: blastn -query GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference/reference_markers.fasta -out GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:08,962] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:08,965] [INFO] Selected 10 target genomes.
[2024-01-25 18:02:08,965] [INFO] Target genome list was writen to GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:08,977] [INFO] Task started: fastANI
[2024-01-25 18:02:08,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg985db758-289c-45bd-934e-dc22631ae821/GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna.gz --refList GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/target_genomes.txt --output GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:21,985] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:21,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:21,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:21,998] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:02:21,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:21,999] [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=B6	GCA_900045375.1	358	358	suspected-type	True	100.0	1943	1946	95	conclusive
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	99.9782	1913	1946	95	conclusive
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	99.944	1850	1946	95	conclusive
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	92.1237	1492	1946	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	90.7422	1373	1946	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	88.9352	1414	1946	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	88.3947	1426	1946	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.5785	630	1946	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.1205	728	1946	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.9679	551	1946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:22,001] [INFO] DFAST Taxonomy check result was written to GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:22,001] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:22,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:22,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference/checkm_data
[2024-01-25 18:02:22,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:22,059] [INFO] Task started: CheckM
[2024-01-25 18:02:22,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/checkm_input GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/checkm_result
[2024-01-25 18:03:07,435] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:07,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:07,455] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:07,456] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:07,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:07,457] [INFO] Task started: Blastn
[2024-01-25 18:03:07,457] [INFO] Running command: blastn -query GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0592157d-eeba-425d-9b41-606389e3e873/dqc_reference/reference_markers_gtdb.fasta -out GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:09,416] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:09,419] [INFO] Selected 14 target genomes.
[2024-01-25 18:03:09,420] [INFO] Target genome list was writen to GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:09,443] [INFO] Task started: fastANI
[2024-01-25 18:03:09,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg985db758-289c-45bd-934e-dc22631ae821/GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna.gz --refList GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:28,742] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:28,751] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:28,751] [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	99.944	1850	1946	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	92.0087	1566	1946	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	90.7422	1373	1946	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	90.5844	1028	1946	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	90.0472	1384	1946	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	89.6626	1452	1946	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	89.5061	1516	1946	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	89.4667	1408	1946	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	89.1082	1502	1946	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	88.9426	1430	1946	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	88.9104	1417	1946	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	88.4809	1423	1946	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	88.3851	1427	1946	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	87.7835	1426	1946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.40	96.96	0.89	0.76	243	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:28,753] [INFO] GTDB search result was written to GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:28,753] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:28,756] [INFO] DFAST_QC result json was written to GCF_900045375.1_AHY_PRJEB12187_v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:28,756] [INFO] DFAST_QC completed!
[2024-01-25 18:03:28,756] [INFO] Total running time: 0h1m38s