[2023-06-30 05:04:27,656] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:04:27,659] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:04:27,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference
[2023-06-30 05:04:29,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:04:29,860] [INFO] Task started: Prodigal
[2023-06-30 05:04:29,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg67e764a5-2163-45dd-a716-2ddfc73c8a41/GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna.gz | prodigal -d GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/cds.fna -a GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:04:40,021] [INFO] Task succeeded: Prodigal
[2023-06-30 05:04:40,022] [INFO] Task started: HMMsearch
[2023-06-30 05:04:40,022] [INFO] Running command: hmmsearch --tblout GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference/reference_markers.hmm GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:04:40,309] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:04:40,312] [INFO] Found 6/6 markers.
[2023-06-30 05:04:40,350] [INFO] Query marker FASTA was written to GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/markers.fasta
[2023-06-30 05:04:40,350] [INFO] Task started: Blastn
[2023-06-30 05:04:40,350] [INFO] Running command: blastn -query GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference/reference_markers.fasta -out GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:41,377] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:41,382] [INFO] Selected 32 target genomes.
[2023-06-30 05:04:41,382] [INFO] Target genome list was writen to GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/target_genomes.txt
[2023-06-30 05:04:41,391] [INFO] Task started: fastANI
[2023-06-30 05:04:41,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e764a5-2163-45dd-a716-2ddfc73c8a41/GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna.gz --refList GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/target_genomes.txt --output GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:05:18,626] [INFO] Task succeeded: fastANI
[2023-06-30 05:05:18,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:05:18,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:05:18,652] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:05:18,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:05:18,653] [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 sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	78.3277	416	1091	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	78.2958	399	1091	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	78.1986	418	1091	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	78.1455	438	1091	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	78.1419	431	1091	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	78.1057	418	1091	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	78.0955	405	1091	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	78.0601	380	1091	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	78.0483	428	1091	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	78.04	425	1091	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	78.0386	409	1091	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	78.0364	400	1091	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	78.0247	367	1091	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	77.983	334	1091	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	77.9715	408	1091	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	77.9531	423	1091	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	77.95	380	1091	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.9454	389	1091	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.9435	440	1091	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	77.9387	421	1091	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	77.9259	450	1091	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	77.9172	428	1091	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	77.9053	408	1091	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.898	404	1091	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	77.8901	396	1091	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	77.8801	432	1091	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	77.8773	409	1091	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	77.848	368	1091	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	77.832	401	1091	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.5725	286	1091	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	77.5315	290	1091	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	77.5298	291	1091	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:05:18,655] [INFO] DFAST Taxonomy check result was written to GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/tc_result.tsv
[2023-06-30 05:05:18,655] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:05:18,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:05:18,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference/checkm_data
[2023-06-30 05:05:18,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:05:18,706] [INFO] Task started: CheckM
[2023-06-30 05:05:18,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/checkm_input GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/checkm_result
[2023-06-30 05:05:54,022] [INFO] Task succeeded: CheckM
[2023-06-30 05:05:54,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:05:54,044] [INFO] ===== Completeness check finished =====
[2023-06-30 05:05:54,044] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:05:54,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/markers.fasta)
[2023-06-30 05:05:54,045] [INFO] Task started: Blastn
[2023-06-30 05:05:54,045] [INFO] Running command: blastn -query GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df8b39a-87a8-47fd-9662-acb6c9fa924f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:05:56,061] [INFO] Task succeeded: Blastn
[2023-06-30 05:05:56,066] [INFO] Selected 13 target genomes.
[2023-06-30 05:05:56,066] [INFO] Target genome list was writen to GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:05:56,074] [INFO] Task started: fastANI
[2023-06-30 05:05:56,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e764a5-2163-45dd-a716-2ddfc73c8a41/GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna.gz --refList GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/target_genomes_gtdb.txt --output GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:06:07,777] [INFO] Task succeeded: fastANI
[2023-06-30 05:06:07,792] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:06:07,792] [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_903839845.1	s__Pseudolabrys sp903839845	99.6906	1007	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.70	99.58	0.91	0.88	17	conclusive
GCA_903892675.1	s__Pseudolabrys sp903892675	89.3892	780	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464835.1	s__Pseudolabrys sp001464835	85.2602	794	1091	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	81.7814	744	1091	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	81.5196	744	1091	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	81.5118	742	1091	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	81.4677	695	1091	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	81.2471	704	1091	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	81.137	696	1091	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	81.0853	697	1091	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	81.0102	684	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.81	99.81	0.96	0.96	2	-
GCF_003367195.1	s__Pseudolabrys sp003367195	80.9577	685	1091	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	80.8967	638	1091	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.84	99.84	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-30 05:06:07,795] [INFO] GTDB search result was written to GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/result_gtdb.tsv
[2023-06-30 05:06:07,796] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:06:07,804] [INFO] DFAST_QC result json was written to GCA_903844065.1_freshwater_MAG_---_KR3_bin-1012_genomic.fna/dqc_result.json
[2023-06-30 05:06:07,805] [INFO] DFAST_QC completed!
[2023-06-30 05:06:07,805] [INFO] Total running time: 0h1m40s