[2024-01-24 14:19:15,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference
[2024-01-24 14:19:18,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,320] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,321] [INFO] Running command: gunzip -c /var/lib/cwl/stgdad95c41-7611-4c7f-8301-ce52bdb5d51e/GCF_002008225.1_ASM200822v1_genomic.fna.gz | prodigal -d GCF_002008225.1_ASM200822v1_genomic.fna/cds.fna -a GCF_002008225.1_ASM200822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:33,563] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:33,564] [INFO] Task started: HMMsearch
[2024-01-24 14:19:33,564] [INFO] Running command: hmmsearch --tblout GCF_002008225.1_ASM200822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference/reference_markers.hmm GCF_002008225.1_ASM200822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:33,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:33,975] [INFO] Found 6/6 markers.
[2024-01-24 14:19:34,019] [INFO] Query marker FASTA was written to GCF_002008225.1_ASM200822v1_genomic.fna/markers.fasta
[2024-01-24 14:19:34,019] [INFO] Task started: Blastn
[2024-01-24 14:19:34,020] [INFO] Running command: blastn -query GCF_002008225.1_ASM200822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference/reference_markers.fasta -out GCF_002008225.1_ASM200822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:35,625] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:35,629] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:35,630] [INFO] Target genome list was writen to GCF_002008225.1_ASM200822v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:35,632] [INFO] Task started: fastANI
[2024-01-24 14:19:35,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgdad95c41-7611-4c7f-8301-ce52bdb5d51e/GCF_002008225.1_ASM200822v1_genomic.fna.gz --refList GCF_002008225.1_ASM200822v1_genomic.fna/target_genomes.txt --output GCF_002008225.1_ASM200822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:50,908] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:50,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:50,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:50,923] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:50,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:50,923] [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 salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	100.0	1642	1645	95	conclusive
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	92.8109	1371	1645	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	90.6862	1365	1645	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	90.6673	1365	1645	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	90.6517	1388	1645	95	below_threshold
Rhizobium pusense	strain=NRCPB10	GCA_002008275.1	648995	648995	type	True	88.2884	1308	1645	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	88.2782	1322	1645	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.4086	687	1645	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.1675	665	1645	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	78.9416	583	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:50,929] [INFO] DFAST Taxonomy check result was written to GCF_002008225.1_ASM200822v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:50,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:50,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:50,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference/checkm_data
[2024-01-24 14:19:50,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:50,996] [INFO] Task started: CheckM
[2024-01-24 14:19:50,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002008225.1_ASM200822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002008225.1_ASM200822v1_genomic.fna/checkm_input GCF_002008225.1_ASM200822v1_genomic.fna/checkm_result
[2024-01-24 14:20:41,566] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:41,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,592] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:41,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:41,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002008225.1_ASM200822v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:41,593] [INFO] Task started: Blastn
[2024-01-24 14:20:41,593] [INFO] Running command: blastn -query GCF_002008225.1_ASM200822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg668da20d-fa57-42f7-9e12-e414e9740982/dqc_reference/reference_markers_gtdb.fasta -out GCF_002008225.1_ASM200822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:44,387] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:44,390] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:44,391] [INFO] Target genome list was writen to GCF_002008225.1_ASM200822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:44,412] [INFO] Task started: fastANI
[2024-01-24 14:20:44,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgdad95c41-7611-4c7f-8301-ce52bdb5d51e/GCF_002008225.1_ASM200822v1_genomic.fna.gz --refList GCF_002008225.1_ASM200822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002008225.1_ASM200822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:59,438] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:59,453] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:59,453] [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_002008225.1	s__Agrobacterium salinitolerans	100.0	1642	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	conclusive
GCF_002943835.1	s__Agrobacterium deltaense	92.527	1390	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	-
GCF_001541315.1	s__Agrobacterium tumefaciens	90.6673	1365	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
GCA_003241215.1	s__Agrobacterium fabrum_A	90.1103	960	1645	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	89.6631	1292	1645	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	89.2845	1360	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_900012615.1	s__Agrobacterium sp900012615	88.967	1299	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	88.4428	1337	1645	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	88.2696	1323	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.39	97.95	0.91	0.74	79	-
GCF_017726655.1	s__Agrobacterium tumefaciens_B	87.5315	1267	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.01	97.83	0.89	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:59,455] [INFO] GTDB search result was written to GCF_002008225.1_ASM200822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:59,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:59,460] [INFO] DFAST_QC result json was written to GCF_002008225.1_ASM200822v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:59,460] [INFO] DFAST_QC completed!
[2024-01-24 14:20:59,460] [INFO] Total running time: 0h1m44s