[2023-06-27 02:56:43,554] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:56:43,557] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:56:43,557] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference
[2023-06-27 02:56:44,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:56:44,802] [INFO] Task started: Prodigal
[2023-06-27 02:56:44,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg586649e9-402b-4767-9cbe-582246015b72/GCA_026400445.1_ASM2640044v1_genomic.fna.gz | prodigal -d GCA_026400445.1_ASM2640044v1_genomic.fna/cds.fna -a GCA_026400445.1_ASM2640044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:56:53,101] [INFO] Task succeeded: Prodigal
[2023-06-27 02:56:53,102] [INFO] Task started: HMMsearch
[2023-06-27 02:56:53,102] [INFO] Running command: hmmsearch --tblout GCA_026400445.1_ASM2640044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference/reference_markers.hmm GCA_026400445.1_ASM2640044v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:56:53,359] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:56:53,360] [INFO] Found 6/6 markers.
[2023-06-27 02:56:53,423] [INFO] Query marker FASTA was written to GCA_026400445.1_ASM2640044v1_genomic.fna/markers.fasta
[2023-06-27 02:56:53,424] [INFO] Task started: Blastn
[2023-06-27 02:56:53,424] [INFO] Running command: blastn -query GCA_026400445.1_ASM2640044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference/reference_markers.fasta -out GCA_026400445.1_ASM2640044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:56:54,348] [INFO] Task succeeded: Blastn
[2023-06-27 02:56:54,353] [INFO] Selected 35 target genomes.
[2023-06-27 02:56:54,354] [INFO] Target genome list was writen to GCA_026400445.1_ASM2640044v1_genomic.fna/target_genomes.txt
[2023-06-27 02:56:54,356] [INFO] Task started: fastANI
[2023-06-27 02:56:54,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg586649e9-402b-4767-9cbe-582246015b72/GCA_026400445.1_ASM2640044v1_genomic.fna.gz --refList GCA_026400445.1_ASM2640044v1_genomic.fna/target_genomes.txt --output GCA_026400445.1_ASM2640044v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:57:31,920] [INFO] Task succeeded: fastANI
[2023-06-27 02:57:31,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:57:31,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:57:31,948] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:57:31,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:57:31,948] [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	78.1035	322	799	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	77.9915	309	799	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	77.9775	323	799	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	77.969	315	799	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	77.9675	325	799	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	77.962	307	799	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.9608	299	799	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	77.9586	305	799	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	77.9524	294	799	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	77.9338	324	799	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.9231	327	799	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	77.9178	289	799	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	77.9173	311	799	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	77.9098	317	799	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	77.8961	317	799	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.8894	319	799	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	77.8781	271	799	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	77.8489	311	799	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	77.8473	336	799	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.7969	290	799	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	77.7674	306	799	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	77.7627	317	799	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	77.7402	322	799	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.7313	298	799	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	77.7042	325	799	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	77.6927	293	799	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	77.6674	326	799	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	77.6268	297	799	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	77.5498	222	799	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.5428	223	799	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	77.5046	226	799	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.3438	234	799	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.2014	207	799	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	77.0036	202	799	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.7402	168	799	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:57:31,964] [INFO] DFAST Taxonomy check result was written to GCA_026400445.1_ASM2640044v1_genomic.fna/tc_result.tsv
[2023-06-27 02:57:31,965] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:57:31,965] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:57:31,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference/checkm_data
[2023-06-27 02:57:31,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:57:32,006] [INFO] Task started: CheckM
[2023-06-27 02:57:32,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400445.1_ASM2640044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400445.1_ASM2640044v1_genomic.fna/checkm_input GCA_026400445.1_ASM2640044v1_genomic.fna/checkm_result
[2023-06-27 02:58:00,442] [INFO] Task succeeded: CheckM
[2023-06-27 02:58:00,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:58:00,479] [INFO] ===== Completeness check finished =====
[2023-06-27 02:58:00,480] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:58:00,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400445.1_ASM2640044v1_genomic.fna/markers.fasta)
[2023-06-27 02:58:00,480] [INFO] Task started: Blastn
[2023-06-27 02:58:00,481] [INFO] Running command: blastn -query GCA_026400445.1_ASM2640044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0b0dc19-9580-4bcd-95ff-9188825a1534/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400445.1_ASM2640044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:58:02,148] [INFO] Task succeeded: Blastn
[2023-06-27 02:58:02,154] [INFO] Selected 13 target genomes.
[2023-06-27 02:58:02,154] [INFO] Target genome list was writen to GCA_026400445.1_ASM2640044v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:58:02,157] [INFO] Task started: fastANI
[2023-06-27 02:58:02,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg586649e9-402b-4767-9cbe-582246015b72/GCA_026400445.1_ASM2640044v1_genomic.fna.gz --refList GCA_026400445.1_ASM2640044v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400445.1_ASM2640044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:58:12,603] [INFO] Task succeeded: fastANI
[2023-06-27 02:58:12,621] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:58:12,622] [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	98.7831	667	799	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	90.1124	712	799	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	85.4082	624	799	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	81.5651	585	799	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	81.4173	588	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	81.2997	552	799	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	81.1999	552	799	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	80.9999	554	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367195.1	s__Pseudolabrys sp003367195	80.9672	529	799	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	80.9379	544	799	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	80.9309	559	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.81	99.81	0.96	0.96	2	-
GCA_903929045.1	s__Pseudolabrys sp903929045	80.8951	520	799	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	79.6933	361	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 02:58:12,625] [INFO] GTDB search result was written to GCA_026400445.1_ASM2640044v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:58:12,625] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:58:12,632] [INFO] DFAST_QC result json was written to GCA_026400445.1_ASM2640044v1_genomic.fna/dqc_result.json
[2023-06-27 02:58:12,632] [INFO] DFAST_QC completed!
[2023-06-27 02:58:12,632] [INFO] Total running time: 0h1m29s