[2024-01-24 14:30:31,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference
[2024-01-24 14:30:33,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,805] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg80f4db64-c5b8-40d2-bd00-dafefe544158/GCF_003367195.1_ASM336719v1_genomic.fna.gz | prodigal -d GCF_003367195.1_ASM336719v1_genomic.fna/cds.fna -a GCF_003367195.1_ASM336719v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:47,172] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:47,172] [INFO] Task started: HMMsearch
[2024-01-24 14:30:47,172] [INFO] Running command: hmmsearch --tblout GCF_003367195.1_ASM336719v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference/reference_markers.hmm GCF_003367195.1_ASM336719v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:47,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:47,549] [INFO] Found 6/6 markers.
[2024-01-24 14:30:47,593] [INFO] Query marker FASTA was written to GCF_003367195.1_ASM336719v1_genomic.fna/markers.fasta
[2024-01-24 14:30:47,593] [INFO] Task started: Blastn
[2024-01-24 14:30:47,594] [INFO] Running command: blastn -query GCF_003367195.1_ASM336719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference/reference_markers.fasta -out GCF_003367195.1_ASM336719v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:48,709] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:48,712] [INFO] Selected 32 target genomes.
[2024-01-24 14:30:48,713] [INFO] Target genome list was writen to GCF_003367195.1_ASM336719v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:48,742] [INFO] Task started: fastANI
[2024-01-24 14:30:48,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f4db64-c5b8-40d2-bd00-dafefe544158/GCF_003367195.1_ASM336719v1_genomic.fna.gz --refList GCF_003367195.1_ASM336719v1_genomic.fna/target_genomes.txt --output GCF_003367195.1_ASM336719v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:25,112] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:25,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:25,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:25,140] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:25,140] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:25,140] [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 diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	78.6301	471	1364	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	78.6264	458	1364	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	78.6118	474	1364	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	78.5729	437	1364	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	78.5245	467	1364	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	78.4988	434	1364	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	78.4871	460	1364	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	78.4829	491	1364	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	78.4736	457	1364	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	78.4732	467	1364	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	78.4669	472	1364	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	78.4481	395	1364	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	78.4317	478	1364	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	78.4292	460	1364	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	78.3941	430	1364	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	78.383	306	1364	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	78.3797	484	1364	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	78.3715	462	1364	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	78.3653	300	1364	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	78.3341	409	1364	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	78.3148	464	1364	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	78.3124	454	1364	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	78.2561	419	1364	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	78.2115	384	1364	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	78.1784	430	1364	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	78.1016	380	1364	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	77.9056	352	1364	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	77.881	349	1364	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.8365	350	1364	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	77.3538	234	1364	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	77.3157	293	1364	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	77.1468	211	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:25,142] [INFO] DFAST Taxonomy check result was written to GCF_003367195.1_ASM336719v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:25,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:25,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:25,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference/checkm_data
[2024-01-24 14:31:25,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:25,189] [INFO] Task started: CheckM
[2024-01-24 14:31:25,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367195.1_ASM336719v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367195.1_ASM336719v1_genomic.fna/checkm_input GCF_003367195.1_ASM336719v1_genomic.fna/checkm_result
[2024-01-24 14:32:05,818] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:05,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,844] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:05,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:05,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367195.1_ASM336719v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:05,846] [INFO] Task started: Blastn
[2024-01-24 14:32:05,846] [INFO] Running command: blastn -query GCF_003367195.1_ASM336719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86b7d6eb-62a7-43df-92f8-b61f577eb5d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367195.1_ASM336719v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:07,873] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:07,878] [INFO] Selected 6 target genomes.
[2024-01-24 14:32:07,878] [INFO] Target genome list was writen to GCF_003367195.1_ASM336719v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:07,884] [INFO] Task started: fastANI
[2024-01-24 14:32:07,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f4db64-c5b8-40d2-bd00-dafefe544158/GCF_003367195.1_ASM336719v1_genomic.fna.gz --refList GCF_003367195.1_ASM336719v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367195.1_ASM336719v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:14,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:14,913] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:14,913] [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_003367195.1	s__Pseudolabrys sp003367195	100.0	1364	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017849615.1	s__Pseudolabrys sp017849615	86.5752	1055	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005153485.1	s__Pseudolabrys sp005153485	86.562	1071	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240595.1	s__Pseudolabrys sp018240595	84.0492	1006	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242205.1	s__Pseudolabrys sp018242205	83.7149	956	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426945.1	s__Pseudolabrys sp001426945	83.6798	1012	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:14,916] [INFO] GTDB search result was written to GCF_003367195.1_ASM336719v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:14,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:14,923] [INFO] DFAST_QC result json was written to GCF_003367195.1_ASM336719v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:14,923] [INFO] DFAST_QC completed!
[2024-01-24 14:32:14,923] [INFO] Total running time: 0h1m44s