[2024-01-25 18:51:50,801] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference
[2024-01-25 18:51:51,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,916] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg6188dc2f-cc08-4129-962e-4cc714abba2d/GCF_000092025.1_ASM9202v1_genomic.fna.gz | prodigal -d GCF_000092025.1_ASM9202v1_genomic.fna/cds.fna -a GCF_000092025.1_ASM9202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:07,499] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:07,499] [INFO] Task started: HMMsearch
[2024-01-25 18:52:07,500] [INFO] Running command: hmmsearch --tblout GCF_000092025.1_ASM9202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference/reference_markers.hmm GCF_000092025.1_ASM9202v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:07,875] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:07,876] [INFO] Found 6/6 markers.
[2024-01-25 18:52:07,923] [INFO] Query marker FASTA was written to GCF_000092025.1_ASM9202v1_genomic.fna/markers.fasta
[2024-01-25 18:52:07,923] [INFO] Task started: Blastn
[2024-01-25 18:52:07,923] [INFO] Running command: blastn -query GCF_000092025.1_ASM9202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference/reference_markers.fasta -out GCF_000092025.1_ASM9202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:08,799] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:08,802] [INFO] Selected 10 target genomes.
[2024-01-25 18:52:08,802] [INFO] Target genome list was writen to GCF_000092025.1_ASM9202v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:08,814] [INFO] Task started: fastANI
[2024-01-25 18:52:08,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg6188dc2f-cc08-4129-962e-4cc714abba2d/GCF_000092025.1_ASM9202v1_genomic.fna.gz --refList GCF_000092025.1_ASM9202v1_genomic.fna/target_genomes.txt --output GCF_000092025.1_ASM9202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:21,316] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:21,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:21,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:21,327] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:52:21,327] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:52:21,327] [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 leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	89.3117	1418	1889	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	89.3016	1376	1889	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	89.1786	1459	1889	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	89.1673	1488	1889	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	89.1659	1468	1889	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	87.8975	1371	1889	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	87.3913	1390	1889	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.0927	608	1889	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	78.9516	683	1889	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.6078	550	1889	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:21,329] [INFO] DFAST Taxonomy check result was written to GCF_000092025.1_ASM9202v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:21,329] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:21,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:21,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference/checkm_data
[2024-01-25 18:52:21,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:21,391] [INFO] Task started: CheckM
[2024-01-25 18:52:21,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092025.1_ASM9202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092025.1_ASM9202v1_genomic.fna/checkm_input GCF_000092025.1_ASM9202v1_genomic.fna/checkm_result
[2024-01-25 18:53:06,410] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:06,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:06,430] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:06,431] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:06,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092025.1_ASM9202v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:06,431] [INFO] Task started: Blastn
[2024-01-25 18:53:06,431] [INFO] Running command: blastn -query GCF_000092025.1_ASM9202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb65dc0a4-608f-4cae-8859-94d23d592843/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092025.1_ASM9202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:08,247] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:08,249] [INFO] Selected 14 target genomes.
[2024-01-25 18:53:08,250] [INFO] Target genome list was writen to GCF_000092025.1_ASM9202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:08,278] [INFO] Task started: fastANI
[2024-01-25 18:53:08,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg6188dc2f-cc08-4129-962e-4cc714abba2d/GCF_000092025.1_ASM9202v1_genomic.fna.gz --refList GCF_000092025.1_ASM9202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092025.1_ASM9202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:27,656] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:27,665] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:27,666] [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_000092025.1	s__Agrobacterium fabrum	100.0	1887	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.52	95.41	0.93	0.85	28	conclusive
GCF_005221325.1	s__Agrobacterium sp900012625	92.1662	1546	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.19	97.65	0.98	0.95	4	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	90.9251	1411	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008225.1	s__Agrobacterium salinitolerans	89.2908	1377	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	-
GCF_001541315.1	s__Agrobacterium tumefaciens	89.1786	1459	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
GCF_002943835.1	s__Agrobacterium deltaense	89.0862	1448	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	88.9523	1410	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_005221385.1	s__Agrobacterium sp900013535	88.6231	1409	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.00	98.18	0.90	0.86	7	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	88.5536	1423	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337285.1	s__Agrobacterium tumefaciens_H	88.469	1397	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	97.88	0.96	0.94	4	-
GCA_000949895.1	s__Agrobacterium arsenijevicii	88.1231	1422	1889	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	87.9135	1373	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCF_000949865.1	s__Agrobacterium nepotum	87.5032	1360	1889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649785.1	s__Agrobacterium fabacearum	87.1929	1449	1889	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 18:53:27,667] [INFO] GTDB search result was written to GCF_000092025.1_ASM9202v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:27,668] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:27,671] [INFO] DFAST_QC result json was written to GCF_000092025.1_ASM9202v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:27,671] [INFO] DFAST_QC completed!
[2024-01-25 18:53:27,671] [INFO] Total running time: 0h1m37s