[2024-01-25 19:46:20,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference
[2024-01-25 19:46:21,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,805] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ca23925-941d-4ee1-8938-9bdc4a3643ef/GCF_002266435.2_ASM226643v2_genomic.fna.gz | prodigal -d GCF_002266435.2_ASM226643v2_genomic.fna/cds.fna -a GCF_002266435.2_ASM226643v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:44,708] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:44,708] [INFO] Task started: HMMsearch
[2024-01-25 19:46:44,708] [INFO] Running command: hmmsearch --tblout GCF_002266435.2_ASM226643v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference/reference_markers.hmm GCF_002266435.2_ASM226643v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:45,054] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:45,055] [INFO] Found 6/6 markers.
[2024-01-25 19:46:45,107] [INFO] Query marker FASTA was written to GCF_002266435.2_ASM226643v2_genomic.fna/markers.fasta
[2024-01-25 19:46:45,108] [INFO] Task started: Blastn
[2024-01-25 19:46:45,108] [INFO] Running command: blastn -query GCF_002266435.2_ASM226643v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference/reference_markers.fasta -out GCF_002266435.2_ASM226643v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:46,165] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:46,168] [INFO] Selected 14 target genomes.
[2024-01-25 19:46:46,168] [INFO] Target genome list was writen to GCF_002266435.2_ASM226643v2_genomic.fna/target_genomes.txt
[2024-01-25 19:46:46,179] [INFO] Task started: fastANI
[2024-01-25 19:46:46,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca23925-941d-4ee1-8938-9bdc4a3643ef/GCF_002266435.2_ASM226643v2_genomic.fna.gz --refList GCF_002266435.2_ASM226643v2_genomic.fna/target_genomes.txt --output GCF_002266435.2_ASM226643v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:16,717] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:16,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:16,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:16,727] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:16,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:16,727] [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
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	100.0	2346	2348	95	conclusive
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	93.9468	2012	2348	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	91.7586	1978	2348	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	91.6699	1939	2348	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	90.5445	2014	2348	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	90.0865	1831	2348	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.8247	1934	2348	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.9226	1832	2348	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.7053	1803	2348	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	88.6146	1746	2348	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.478	1833	2348	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	88.4387	1809	2348	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9612	1426	2348	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.9236	1329	2348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:16,728] [INFO] DFAST Taxonomy check result was written to GCF_002266435.2_ASM226643v2_genomic.fna/tc_result.tsv
[2024-01-25 19:47:16,729] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:16,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:16,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference/checkm_data
[2024-01-25 19:47:16,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:16,796] [INFO] Task started: CheckM
[2024-01-25 19:47:16,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002266435.2_ASM226643v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002266435.2_ASM226643v2_genomic.fna/checkm_input GCF_002266435.2_ASM226643v2_genomic.fna/checkm_result
[2024-01-25 19:48:30,366] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:30,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:30,385] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:30,385] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:30,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002266435.2_ASM226643v2_genomic.fna/markers.fasta)
[2024-01-25 19:48:30,387] [INFO] Task started: Blastn
[2024-01-25 19:48:30,387] [INFO] Running command: blastn -query GCF_002266435.2_ASM226643v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg85e9e71b-d636-4b2a-abb8-32b10f8b8e2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002266435.2_ASM226643v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:32,665] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:32,668] [INFO] Selected 12 target genomes.
[2024-01-25 19:48:32,668] [INFO] Target genome list was writen to GCF_002266435.2_ASM226643v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:32,678] [INFO] Task started: fastANI
[2024-01-25 19:48:32,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca23925-941d-4ee1-8938-9bdc4a3643ef/GCF_002266435.2_ASM226643v2_genomic.fna.gz --refList GCF_002266435.2_ASM226643v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002266435.2_ASM226643v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:58,729] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:58,737] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:58,737] [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_002266435.2	s__Bradyrhizobium amphicarpaeae	100.0	2346	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002266465.2	s__Bradyrhizobium symbiodeficiens	93.9398	2012	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.63	98.60	0.94	0.93	4	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	93.4015	2060	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129985.1	s__Bradyrhizobium japonicum_H	92.7503	1991	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278135.2	s__Bradyrhizobium ottawaense	91.7591	1977	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.77	95.31	0.93	0.88	13	-
GCF_900094605.1	s__Bradyrhizobium shewense	91.666	1940	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	91.6283	1925	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	90.547	2014	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	90.5163	2022	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291745.1	s__Bradyrhizobium sp015291745	90.137	1933	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	97.81	0.93	0.92	4	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.3283	1864	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	88.9212	1865	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:58,738] [INFO] GTDB search result was written to GCF_002266435.2_ASM226643v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:58,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:58,742] [INFO] DFAST_QC result json was written to GCF_002266435.2_ASM226643v2_genomic.fna/dqc_result.json
[2024-01-25 19:48:58,742] [INFO] DFAST_QC completed!
[2024-01-25 19:48:58,742] [INFO] Total running time: 0h2m38s