[2023-06-28 21:02:28,961] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:02:28,966] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:02:28,966] [INFO] DQC Reference Directory: /var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference
[2023-06-28 21:02:30,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:02:30,292] [INFO] Task started: Prodigal
[2023-06-28 21:02:30,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg2de908a9-8a97-4b1e-a2b6-ab8e8e790fac/GCA_019243075.1_ASM1924307v1_genomic.fna.gz | prodigal -d GCA_019243075.1_ASM1924307v1_genomic.fna/cds.fna -a GCA_019243075.1_ASM1924307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:02:40,147] [INFO] Task succeeded: Prodigal
[2023-06-28 21:02:40,147] [INFO] Task started: HMMsearch
[2023-06-28 21:02:40,147] [INFO] Running command: hmmsearch --tblout GCA_019243075.1_ASM1924307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference/reference_markers.hmm GCA_019243075.1_ASM1924307v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:02:40,410] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:02:40,412] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2de908a9-8a97-4b1e-a2b6-ab8e8e790fac/GCA_019243075.1_ASM1924307v1_genomic.fna.gz]
[2023-06-28 21:02:40,453] [INFO] Query marker FASTA was written to GCA_019243075.1_ASM1924307v1_genomic.fna/markers.fasta
[2023-06-28 21:02:40,454] [INFO] Task started: Blastn
[2023-06-28 21:02:40,454] [INFO] Running command: blastn -query GCA_019243075.1_ASM1924307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference/reference_markers.fasta -out GCA_019243075.1_ASM1924307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:41,136] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:41,140] [INFO] Selected 14 target genomes.
[2023-06-28 21:02:41,140] [INFO] Target genome list was writen to GCA_019243075.1_ASM1924307v1_genomic.fna/target_genomes.txt
[2023-06-28 21:02:41,142] [INFO] Task started: fastANI
[2023-06-28 21:02:41,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg2de908a9-8a97-4b1e-a2b6-ab8e8e790fac/GCA_019243075.1_ASM1924307v1_genomic.fna.gz --refList GCA_019243075.1_ASM1924307v1_genomic.fna/target_genomes.txt --output GCA_019243075.1_ASM1924307v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:03:02,556] [INFO] Task succeeded: fastANI
[2023-06-28 21:03:02,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:03:02,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:03:02,569] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:03:02,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:03:02,569] [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 mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	81.8106	702	1013	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	81.5754	728	1013	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	81.499	679	1013	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	81.4942	665	1013	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	81.4942	714	1013	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	81.4657	699	1013	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	81.3961	649	1013	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	81.385	588	1013	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	81.3819	673	1013	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	81.3452	669	1013	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	81.2962	697	1013	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	81.1679	683	1013	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	80.8908	666	1013	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	80.5688	624	1013	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:03:02,572] [INFO] DFAST Taxonomy check result was written to GCA_019243075.1_ASM1924307v1_genomic.fna/tc_result.tsv
[2023-06-28 21:03:02,572] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:03:02,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:03:02,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference/checkm_data
[2023-06-28 21:03:02,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:03:02,622] [INFO] Task started: CheckM
[2023-06-28 21:03:02,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019243075.1_ASM1924307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019243075.1_ASM1924307v1_genomic.fna/checkm_input GCA_019243075.1_ASM1924307v1_genomic.fna/checkm_result
[2023-06-28 21:03:34,425] [INFO] Task succeeded: CheckM
[2023-06-28 21:03:34,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:03:34,453] [INFO] ===== Completeness check finished =====
[2023-06-28 21:03:34,454] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:03:34,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019243075.1_ASM1924307v1_genomic.fna/markers.fasta)
[2023-06-28 21:03:34,455] [INFO] Task started: Blastn
[2023-06-28 21:03:34,455] [INFO] Running command: blastn -query GCA_019243075.1_ASM1924307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc31edad5-f258-4f3e-8865-86932b9d407d/dqc_reference/reference_markers_gtdb.fasta -out GCA_019243075.1_ASM1924307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:03:35,180] [INFO] Task succeeded: Blastn
[2023-06-28 21:03:35,186] [INFO] Selected 12 target genomes.
[2023-06-28 21:03:35,187] [INFO] Target genome list was writen to GCA_019243075.1_ASM1924307v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:03:35,202] [INFO] Task started: fastANI
[2023-06-28 21:03:35,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg2de908a9-8a97-4b1e-a2b6-ab8e8e790fac/GCA_019243075.1_ASM1924307v1_genomic.fna.gz --refList GCA_019243075.1_ASM1924307v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019243075.1_ASM1924307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:03:51,416] [INFO] Task succeeded: fastANI
[2023-06-28 21:03:51,433] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:03:51,434] [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
GCA_019243075.1	s__Bradyrhizobium sp019243075	100.0	996	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019242285.1	s__Bradyrhizobium sp019242285	81.605	677	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472425.1	s__Bradyrhizobium sp000472425	81.5386	699	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795245.1	s__Bradyrhizobium forestalis	81.5223	661	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472865.1	s__Bradyrhizobium elkanii_A	81.3955	691	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.78	96.35	0.83	0.83	3	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	81.3843	688	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	81.3655	689	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_015291665.1	s__Bradyrhizobium sp015291665	81.2109	664	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130385.1	s__Bradyrhizobium sp018130385	81.07	651	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884765.1	s__Bradyrhizobium sp005884765	80.8768	643	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472385.1	s__Bradyrhizobium sp000472385	80.7135	675	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701345.1	s__Bradyrhizobium sp000701345	79.7566	534	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:03:51,436] [INFO] GTDB search result was written to GCA_019243075.1_ASM1924307v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:03:51,437] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:03:51,442] [INFO] DFAST_QC result json was written to GCA_019243075.1_ASM1924307v1_genomic.fna/dqc_result.json
[2023-06-28 21:03:51,442] [INFO] DFAST_QC completed!
[2023-06-28 21:03:51,443] [INFO] Total running time: 0h1m22s