[2024-01-24 13:27:25,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:25,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:25,286] [INFO] DQC Reference Directory: /var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference
[2024-01-24 13:27:26,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:26,458] [INFO] Task started: Prodigal
[2024-01-24 13:27:26,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg94d51a76-08b5-4aeb-acca-8e2dc366300e/GCF_014203115.1_ASM1420311v1_genomic.fna.gz | prodigal -d GCF_014203115.1_ASM1420311v1_genomic.fna/cds.fna -a GCF_014203115.1_ASM1420311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:42,369] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:42,370] [INFO] Task started: HMMsearch
[2024-01-24 13:27:42,370] [INFO] Running command: hmmsearch --tblout GCF_014203115.1_ASM1420311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference/reference_markers.hmm GCF_014203115.1_ASM1420311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:42,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:42,684] [INFO] Found 6/6 markers.
[2024-01-24 13:27:42,731] [INFO] Query marker FASTA was written to GCF_014203115.1_ASM1420311v1_genomic.fna/markers.fasta
[2024-01-24 13:27:42,732] [INFO] Task started: Blastn
[2024-01-24 13:27:42,732] [INFO] Running command: blastn -query GCF_014203115.1_ASM1420311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference/reference_markers.fasta -out GCF_014203115.1_ASM1420311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:43,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:43,718] [INFO] Selected 14 target genomes.
[2024-01-24 13:27:43,718] [INFO] Target genome list was writen to GCF_014203115.1_ASM1420311v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:43,768] [INFO] Task started: fastANI
[2024-01-24 13:27:43,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d51a76-08b5-4aeb-acca-8e2dc366300e/GCF_014203115.1_ASM1420311v1_genomic.fna.gz --refList GCF_014203115.1_ASM1420311v1_genomic.fna/target_genomes.txt --output GCF_014203115.1_ASM1420311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:02,696] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:02,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:02,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:02,718] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:02,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:02,719] [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
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	100.0	1766	1766	95	conclusive
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	89.4444	1307	1766	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	85.8486	1223	1766	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	84.6588	1153	1766	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	80.0263	788	1766	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	79.908	578	1766	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.8968	790	1766	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	79.8472	699	1766	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	79.7992	767	1766	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.7437	752	1766	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	79.7144	742	1766	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	79.6948	785	1766	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	79.6324	747	1766	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	79.5529	747	1766	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:02,721] [INFO] DFAST Taxonomy check result was written to GCF_014203115.1_ASM1420311v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:02,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:02,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:02,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference/checkm_data
[2024-01-24 13:28:02,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:02,777] [INFO] Task started: CheckM
[2024-01-24 13:28:02,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203115.1_ASM1420311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203115.1_ASM1420311v1_genomic.fna/checkm_input GCF_014203115.1_ASM1420311v1_genomic.fna/checkm_result
[2024-01-24 13:28:51,625] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:51,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:51,655] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:51,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:51,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203115.1_ASM1420311v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:51,656] [INFO] Task started: Blastn
[2024-01-24 13:28:51,656] [INFO] Running command: blastn -query GCF_014203115.1_ASM1420311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6e3f7ce-a2ed-49fa-97f1-2c55b6477ae1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203115.1_ASM1420311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:53,687] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:53,690] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:53,691] [INFO] Target genome list was writen to GCF_014203115.1_ASM1420311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:53,703] [INFO] Task started: fastANI
[2024-01-24 13:28:53,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d51a76-08b5-4aeb-acca-8e2dc366300e/GCF_014203115.1_ASM1420311v1_genomic.fna.gz --refList GCF_014203115.1_ASM1420311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203115.1_ASM1420311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:05,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:05,557] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:05,557] [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_014203115.1	s__Afipia massiliensis	100.0	1766	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001006325.2	s__Afipia massiliensis_A	94.6792	1344	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308295.2	s__Afipia birgiae	89.4462	1307	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.96	98.31	0.86	0.83	3	-
GCA_017474385.1	s__Afipia sp017474385	86.8913	991	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497575.1	s__Afipia sp000497575	86.0211	1201	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	-
GCF_000314675.2	s__Afipia broomeae	85.8684	1222	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	-
GCF_000336555.1	s__Afipia clevelandensis	84.6603	1152	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.84	97.84	0.91	0.91	2	-
GCA_017308595.1	s__Afipia sp017308595	84.1721	1134	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308495.1	s__Afipia sp017308495	82.3607	761	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,564] [INFO] GTDB search result was written to GCF_014203115.1_ASM1420311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:05,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:05,568] [INFO] DFAST_QC result json was written to GCF_014203115.1_ASM1420311v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:05,568] [INFO] DFAST_QC completed!
[2024-01-24 13:29:05,568] [INFO] Total running time: 0h1m40s