[2023-06-14 01:07:23,472] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:07:23,474] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:07:23,474] [INFO] DQC Reference Directory: /var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference
[2023-06-14 01:07:24,721] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:07:24,722] [INFO] Task started: Prodigal
[2023-06-14 01:07:24,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3e5fa26-37bd-4560-ba5d-6dcd4b70b7a3/GCA_947482245.1_RH-9nov16-120_genomic.fna.gz | prodigal -d GCA_947482245.1_RH-9nov16-120_genomic.fna/cds.fna -a GCA_947482245.1_RH-9nov16-120_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:32,419] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:32,420] [INFO] Task started: HMMsearch
[2023-06-14 01:07:32,420] [INFO] Running command: hmmsearch --tblout GCA_947482245.1_RH-9nov16-120_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference/reference_markers.hmm GCA_947482245.1_RH-9nov16-120_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:32,665] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:32,667] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb3e5fa26-37bd-4560-ba5d-6dcd4b70b7a3/GCA_947482245.1_RH-9nov16-120_genomic.fna.gz]
[2023-06-14 01:07:32,699] [INFO] Query marker FASTA was written to GCA_947482245.1_RH-9nov16-120_genomic.fna/markers.fasta
[2023-06-14 01:07:32,700] [INFO] Task started: Blastn
[2023-06-14 01:07:32,700] [INFO] Running command: blastn -query GCA_947482245.1_RH-9nov16-120_genomic.fna/markers.fasta -db /var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference/reference_markers.fasta -out GCA_947482245.1_RH-9nov16-120_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:33,339] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:33,344] [INFO] Selected 29 target genomes.
[2023-06-14 01:07:33,345] [INFO] Target genome list was writen to GCA_947482245.1_RH-9nov16-120_genomic.fna/target_genomes.txt
[2023-06-14 01:07:33,354] [INFO] Task started: fastANI
[2023-06-14 01:07:33,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e5fa26-37bd-4560-ba5d-6dcd4b70b7a3/GCA_947482245.1_RH-9nov16-120_genomic.fna.gz --refList GCA_947482245.1_RH-9nov16-120_genomic.fna/target_genomes.txt --output GCA_947482245.1_RH-9nov16-120_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:08:02,744] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:02,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:08:02,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:08:02,774] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:08:02,774] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:08:02,774] [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 elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	77.8934	297	851	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.8714	305	851	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.8253	304	851	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	77.7564	297	851	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	77.6715	293	851	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.5986	312	851	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	77.5929	301	851	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	77.5807	304	851	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	77.5636	221	851	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	77.563	245	851	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	77.5199	293	851	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	77.4883	302	851	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	77.4553	298	851	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	77.4496	306	851	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	77.4488	298	851	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	77.4449	295	851	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.4232	299	851	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	77.422	199	851	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	77.4125	239	851	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	77.3885	267	851	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	77.3835	200	851	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.3419	295	851	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.3365	305	851	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.2551	225	851	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.6713	173	851	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.5406	154	851	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.4673	180	851	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	76.3655	121	851	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.3192	182	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:08:02,776] [INFO] DFAST Taxonomy check result was written to GCA_947482245.1_RH-9nov16-120_genomic.fna/tc_result.tsv
[2023-06-14 01:08:02,777] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:08:02,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:08:02,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference/checkm_data
[2023-06-14 01:08:02,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:08:02,814] [INFO] Task started: CheckM
[2023-06-14 01:08:02,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947482245.1_RH-9nov16-120_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947482245.1_RH-9nov16-120_genomic.fna/checkm_input GCA_947482245.1_RH-9nov16-120_genomic.fna/checkm_result
[2023-06-14 01:08:30,000] [INFO] Task succeeded: CheckM
[2023-06-14 01:08:30,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:08:30,026] [INFO] ===== Completeness check finished =====
[2023-06-14 01:08:30,026] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:08:30,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947482245.1_RH-9nov16-120_genomic.fna/markers.fasta)
[2023-06-14 01:08:30,027] [INFO] Task started: Blastn
[2023-06-14 01:08:30,027] [INFO] Running command: blastn -query GCA_947482245.1_RH-9nov16-120_genomic.fna/markers.fasta -db /var/lib/cwl/stgc80887d4-2528-4086-90d8-41ce03ef8837/dqc_reference/reference_markers_gtdb.fasta -out GCA_947482245.1_RH-9nov16-120_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:08:31,037] [INFO] Task succeeded: Blastn
[2023-06-14 01:08:31,041] [INFO] Selected 14 target genomes.
[2023-06-14 01:08:31,041] [INFO] Target genome list was writen to GCA_947482245.1_RH-9nov16-120_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:08:31,085] [INFO] Task started: fastANI
[2023-06-14 01:08:31,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e5fa26-37bd-4560-ba5d-6dcd4b70b7a3/GCA_947482245.1_RH-9nov16-120_genomic.fna.gz --refList GCA_947482245.1_RH-9nov16-120_genomic.fna/target_genomes_gtdb.txt --output GCA_947482245.1_RH-9nov16-120_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:08:43,144] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:43,160] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:08:43,160] [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_903892675.1	s__Pseudolabrys sp903892675	99.2919	695	851	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_903839845.1	s__Pseudolabrys sp903839845	89.7422	721	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.70	99.58	0.91	0.88	17	-
GCA_001464835.1	s__Pseudolabrys sp001464835	84.9009	630	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878085.1	s__Pseudolabrys sp903878085	81.2272	599	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.95	99.95	0.96	0.96	2	-
GCA_016124795.1	s__Pseudolabrys sp016124795	81.216	594	851	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	81.0888	572	851	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	81.0078	543	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849615.1	s__Pseudolabrys sp017849615	80.9984	561	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885555.1	s__Pseudolabrys sp903885555	80.8827	554	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.81	99.81	0.96	0.96	2	-
GCA_016185205.1	s__Pseudolabrys sp016185205	80.8696	570	851	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	80.648	542	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929045.1	s__Pseudolabrys sp903929045	80.5787	510	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.84	99.84	0.87	0.87	2	-
GCA_903891395.1	s__Pseudolabrys sp903891395	79.8219	362	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899255.1	s__62-47 sp001899255	77.4687	236	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__62-47	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-14 01:08:43,162] [INFO] GTDB search result was written to GCA_947482245.1_RH-9nov16-120_genomic.fna/result_gtdb.tsv
[2023-06-14 01:08:43,163] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:08:43,167] [INFO] DFAST_QC result json was written to GCA_947482245.1_RH-9nov16-120_genomic.fna/dqc_result.json
[2023-06-14 01:08:43,168] [INFO] DFAST_QC completed!
[2023-06-14 01:08:43,168] [INFO] Total running time: 0h1m20s