[2024-01-24 12:14:34,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference
[2024-01-24 12:14:35,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,414] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,414] [INFO] Running command: gunzip -c /var/lib/cwl/stg5264ca38-b8aa-46ba-a6d5-e4cedbda90b5/GCF_002266465.2_ASM226646v2_genomic.fna.gz | prodigal -d GCF_002266465.2_ASM226646v2_genomic.fna/cds.fna -a GCF_002266465.2_ASM226646v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:54,661] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:54,661] [INFO] Task started: HMMsearch
[2024-01-24 12:14:54,661] [INFO] Running command: hmmsearch --tblout GCF_002266465.2_ASM226646v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference/reference_markers.hmm GCF_002266465.2_ASM226646v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:55,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:55,072] [INFO] Found 6/6 markers.
[2024-01-24 12:14:55,132] [INFO] Query marker FASTA was written to GCF_002266465.2_ASM226646v2_genomic.fna/markers.fasta
[2024-01-24 12:14:55,132] [INFO] Task started: Blastn
[2024-01-24 12:14:55,133] [INFO] Running command: blastn -query GCF_002266465.2_ASM226646v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference/reference_markers.fasta -out GCF_002266465.2_ASM226646v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,156] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,158] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:56,159] [INFO] Target genome list was writen to GCF_002266465.2_ASM226646v2_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,163] [INFO] Task started: fastANI
[2024-01-24 12:14:56,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg5264ca38-b8aa-46ba-a6d5-e4cedbda90b5/GCF_002266465.2_ASM226646v2_genomic.fna.gz --refList GCF_002266465.2_ASM226646v2_genomic.fna/target_genomes.txt --output GCF_002266465.2_ASM226646v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:28,539] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:28,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:28,549] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:28,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:28,550] [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 symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	100.0	2345	2346	95	conclusive
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	93.918	2002	2346	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	92.0616	1943	2346	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	91.9252	1901	2346	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	90.5711	1946	2346	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.7865	1924	2346	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.3521	1846	2346	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.1815	1821	2346	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.9879	1784	2346	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	88.9848	1808	2346	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.8152	1800	2346	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	88.6388	1831	2346	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.4498	1831	2346	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9156	1418	2346	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8678	1327	2346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,551] [INFO] DFAST Taxonomy check result was written to GCF_002266465.2_ASM226646v2_genomic.fna/tc_result.tsv
[2024-01-24 12:15:28,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:28,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:28,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference/checkm_data
[2024-01-24 12:15:28,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:28,619] [INFO] Task started: CheckM
[2024-01-24 12:15:28,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002266465.2_ASM226646v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002266465.2_ASM226646v2_genomic.fna/checkm_input GCF_002266465.2_ASM226646v2_genomic.fna/checkm_result
[2024-01-24 12:16:27,762] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:27,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:27,777] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:27,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:27,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002266465.2_ASM226646v2_genomic.fna/markers.fasta)
[2024-01-24 12:16:27,778] [INFO] Task started: Blastn
[2024-01-24 12:16:27,778] [INFO] Running command: blastn -query GCF_002266465.2_ASM226646v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d79abfd-69ce-4aec-b097-6f265806419d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002266465.2_ASM226646v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:29,844] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:29,846] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:29,846] [INFO] Target genome list was writen to GCF_002266465.2_ASM226646v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:29,852] [INFO] Task started: fastANI
[2024-01-24 12:16:29,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg5264ca38-b8aa-46ba-a6d5-e4cedbda90b5/GCF_002266465.2_ASM226646v2_genomic.fna.gz --refList GCF_002266465.2_ASM226646v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002266465.2_ASM226646v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:50,579] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:50,586] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:50,586] [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_002266465.2	s__Bradyrhizobium symbiodeficiens	100.0	2346	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.63	98.60	0.94	0.93	4	conclusive
GCF_003020125.1	s__Bradyrhizobium sp003020125	94.7637	2033	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266435.2	s__Bradyrhizobium amphicarpaeae	93.918	2002	2346	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	93.6385	1959	2346	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	92.0615	1943	2346	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	91.9268	1901	2346	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	91.8578	1894	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_018131185.1	s__Bradyrhizobium diazoefficiens_G	89.8466	1850	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.4356	1836	2346	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	88.9526	1830	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:50,588] [INFO] GTDB search result was written to GCF_002266465.2_ASM226646v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:50,588] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:50,592] [INFO] DFAST_QC result json was written to GCF_002266465.2_ASM226646v2_genomic.fna/dqc_result.json
[2024-01-24 12:16:50,592] [INFO] DFAST_QC completed!
[2024-01-24 12:16:50,592] [INFO] Total running time: 0h2m16s