[2023-03-17 07:28:31,296] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,296] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference
[2023-03-17 07:28:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,080] [INFO] Running command: cat /var/lib/cwl/stg2b463c26-9fe4-4512-a9c7-1bf4caa6c628/OceanDNA-b27517.fa | prodigal -d OceanDNA-b27517/cds.fna -a OceanDNA-b27517/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:29:07,584] [INFO] Task succeeded: Prodigal
[2023-03-17 07:29:07,584] [INFO] Task started: HMMsearch
[2023-03-17 07:29:07,584] [INFO] Running command: hmmsearch --tblout OceanDNA-b27517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference/reference_markers.hmm OceanDNA-b27517/protein.faa > /dev/null
[2023-03-17 07:29:07,866] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:29:07,867] [INFO] Found 6/6 markers.
[2023-03-17 07:29:07,910] [INFO] Query marker FASTA was written to OceanDNA-b27517/markers.fasta
[2023-03-17 07:29:07,910] [INFO] Task started: Blastn
[2023-03-17 07:29:07,910] [INFO] Running command: blastn -query OceanDNA-b27517/markers.fasta -db /var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference/reference_markers.fasta -out OceanDNA-b27517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:08,777] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:08,778] [INFO] Selected 28 target genomes.
[2023-03-17 07:29:08,778] [INFO] Target genome list was writen to OceanDNA-b27517/target_genomes.txt
[2023-03-17 07:29:08,795] [INFO] Task started: fastANI
[2023-03-17 07:29:08,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b463c26-9fe4-4512-a9c7-1bf4caa6c628/OceanDNA-b27517.fa --refList OceanDNA-b27517/target_genomes.txt --output OceanDNA-b27517/fastani_result.tsv --threads 1
[2023-03-17 07:29:41,256] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:41,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:41,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:41,272] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:41,272] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:29:41,272] [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
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	80.2287	936	1832	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	80.2269	925	1832	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.9577	436	1832	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	77.9229	417	1832	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.9209	500	1832	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	77.8634	481	1832	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.8605	455	1832	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	77.8602	464	1832	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	77.8374	483	1832	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	77.7869	426	1832	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.7531	467	1832	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	77.7485	436	1832	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.6674	476	1832	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.6394	447	1832	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	77.6375	363	1832	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	77.6366	415	1832	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	77.6283	475	1832	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.6027	396	1832	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.5962	463	1832	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	77.5752	474	1832	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	77.4925	468	1832	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.4194	362	1832	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	77.3485	349	1832	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	77.2461	309	1832	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	77.2386	308	1832	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.2299	311	1832	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.0678	364	1832	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	76.9463	216	1832	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:29:41,272] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27517/tc_result.tsv
[2023-03-17 07:29:41,273] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:41,273] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:41,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference/checkm_data
[2023-03-17 07:29:41,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:41,281] [INFO] Task started: CheckM
[2023-03-17 07:29:41,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27517/checkm_input OceanDNA-b27517/checkm_result
[2023-03-17 07:31:03,124] [INFO] Task succeeded: CheckM
[2023-03-17 07:31:03,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:31:03,128] [INFO] ===== Completeness check finished =====
[2023-03-17 07:31:03,129] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:31:03,129] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27517/markers.fasta)
[2023-03-17 07:31:03,130] [INFO] Task started: Blastn
[2023-03-17 07:31:03,130] [INFO] Running command: blastn -query OceanDNA-b27517/markers.fasta -db /var/lib/cwl/stg44db3df4-a236-4c64-afc5-3484239b4ab1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:31:04,630] [INFO] Task succeeded: Blastn
[2023-03-17 07:31:04,631] [INFO] Selected 22 target genomes.
[2023-03-17 07:31:04,631] [INFO] Target genome list was writen to OceanDNA-b27517/target_genomes_gtdb.txt
[2023-03-17 07:31:05,068] [INFO] Task started: fastANI
[2023-03-17 07:31:05,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b463c26-9fe4-4512-a9c7-1bf4caa6c628/OceanDNA-b27517.fa --refList OceanDNA-b27517/target_genomes_gtdb.txt --output OceanDNA-b27517/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:31:25,177] [INFO] Task succeeded: fastANI
[2023-03-17 07:31:25,190] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:31:25,190] [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_002119765.1	s__Pseudorhodoplanes sinuspersici	80.2576	920	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013388965.1	s__Pseudorhodoplanes sp013388965	79.6307	557	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	79.422	558	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCA_008933495.1	s__Pseudorhodoplanes sp008933495	79.2133	398	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899285.1	s__Pseudolabrys sp001899285	78.7639	531	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.99	99.99	1.00	1.00	2	-
GCA_009694215.1	s__Z2-YC6860 sp009694215	78.4358	380	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297465.1	s__SCUB01 sp004297465	78.3628	385	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__SCUB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878085.1	s__Pseudolabrys sp903878085	78.3432	503	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.95	99.95	0.96	0.96	2	-
GCA_018242205.1	s__Pseudolabrys sp018242205	78.2549	462	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884685.1	s__PALSA-894 sp005884685	78.1635	470	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	78.1238	425	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014825.1	s__Rhodopseudomonas palustris_B	77.9863	420	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579845.1	s__Z2-YC6860 sp001579845	77.983	574	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110435.1	s__Rhodopseudomonas pseudopalustris	77.9391	415	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.41	98.34	0.90	0.86	3	-
GCA_009377755.1	s__WHTM01 sp009377755	77.9012	428	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__WHTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449525.1	s__Bradyrhizobium sp018449525	77.7242	381	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344805.1	s__Bradyrhizobium oligotrophicum	77.723	449	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	77.6547	487	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591005.1	s__Rhodopseudomonas palustris_K	77.5903	449	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971625.1	s__Bradyrhizobium sp018971625	77.2685	248	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364445.2	s__Methylobacterium mesophilicum	76.6913	223	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000895.1	s__Methylobacterium sp008000895	76.4205	234	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	98.22	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-17 07:31:25,190] [INFO] GTDB search result was written to OceanDNA-b27517/result_gtdb.tsv
[2023-03-17 07:31:25,190] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:31:25,193] [INFO] DFAST_QC result json was written to OceanDNA-b27517/dqc_result.json
[2023-03-17 07:31:25,193] [INFO] DFAST_QC completed!
[2023-03-17 07:31:25,193] [INFO] Total running time: 0h2m54s