[2023-03-17 09:33:09,714] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,715] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference
[2023-03-17 09:33:10,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:10,830] [INFO] Task started: Prodigal
[2023-03-17 09:33:10,830] [INFO] Running command: cat /var/lib/cwl/stg8da1076e-7af6-4385-b7fe-8d4bacc02339/OceanDNA-b26864.fa | prodigal -d OceanDNA-b26864/cds.fna -a OceanDNA-b26864/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:37,583] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:37,583] [INFO] Task started: HMMsearch
[2023-03-17 09:33:37,583] [INFO] Running command: hmmsearch --tblout OceanDNA-b26864/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference/reference_markers.hmm OceanDNA-b26864/protein.faa > /dev/null
[2023-03-17 09:33:37,799] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:37,799] [INFO] Found 6/6 markers.
[2023-03-17 09:33:37,825] [INFO] Query marker FASTA was written to OceanDNA-b26864/markers.fasta
[2023-03-17 09:33:37,826] [INFO] Task started: Blastn
[2023-03-17 09:33:37,826] [INFO] Running command: blastn -query OceanDNA-b26864/markers.fasta -db /var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference/reference_markers.fasta -out OceanDNA-b26864/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:38,653] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:38,654] [INFO] Selected 20 target genomes.
[2023-03-17 09:33:38,654] [INFO] Target genome list was writen to OceanDNA-b26864/target_genomes.txt
[2023-03-17 09:33:38,887] [INFO] Task started: fastANI
[2023-03-17 09:33:38,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da1076e-7af6-4385-b7fe-8d4bacc02339/OceanDNA-b26864.fa --refList OceanDNA-b26864/target_genomes.txt --output OceanDNA-b26864/fastani_result.tsv --threads 1
[2023-03-17 09:33:59,818] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:59,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:59,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:59,830] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:59,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:33:59,830] [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
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	79.411	586	1422	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	78.9801	512	1422	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	78.8131	560	1422	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.2879	454	1422	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.2775	401	1422	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.2742	430	1422	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	78.2278	440	1422	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	78.2149	431	1422	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	78.1537	407	1422	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	77.9713	311	1422	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.9704	389	1422	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	77.9571	403	1422	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	77.9115	366	1422	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.7515	325	1422	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	77.7409	370	1422	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.7046	310	1422	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.6044	374	1422	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.5731	366	1422	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.4179	289	1422	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.4077	290	1422	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:33:59,831] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26864/tc_result.tsv
[2023-03-17 09:33:59,831] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:59,831] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:59,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference/checkm_data
[2023-03-17 09:33:59,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:59,837] [INFO] Task started: CheckM
[2023-03-17 09:33:59,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26864/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26864/checkm_input OceanDNA-b26864/checkm_result
[2023-03-17 09:35:06,056] [INFO] Task succeeded: CheckM
[2023-03-17 09:35:06,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:35:06,060] [INFO] ===== Completeness check finished =====
[2023-03-17 09:35:06,060] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:35:06,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26864/markers.fasta)
[2023-03-17 09:35:06,061] [INFO] Task started: Blastn
[2023-03-17 09:35:06,061] [INFO] Running command: blastn -query OceanDNA-b26864/markers.fasta -db /var/lib/cwl/stg5ad540e9-6ecc-4fa5-90ed-31b9fcc1ee9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26864/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:35:07,605] [INFO] Task succeeded: Blastn
[2023-03-17 09:35:07,606] [INFO] Selected 13 target genomes.
[2023-03-17 09:35:07,606] [INFO] Target genome list was writen to OceanDNA-b26864/target_genomes_gtdb.txt
[2023-03-17 09:35:08,119] [INFO] Task started: fastANI
[2023-03-17 09:35:08,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da1076e-7af6-4385-b7fe-8d4bacc02339/OceanDNA-b26864.fa --refList OceanDNA-b26864/target_genomes_gtdb.txt --output OceanDNA-b26864/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:35:20,128] [INFO] Task succeeded: fastANI
[2023-03-17 09:35:20,137] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:35:20,137] [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_002707605.1	s__Pseudohoeflea sp002707605	99.3982	1411	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	98.85	97.79	0.96	0.89	4	conclusive
GCF_004354915.1	s__Pseudohoeflea suaedae	87.5701	1042	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709005.1	s__Pseudohoeflea sp002709005	83.7574	866	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	79.4066	587	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	79.2004	589	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	78.8598	332	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	78.7846	522	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_902498795.1	s__Hoeflea sp902498795	78.6868	512	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCA_002733955.1	s__Hoeflea sp002733955	78.5952	502	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	78.2365	439	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282095.2	s__Neorhizobium sp000282095	78.1004	375	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	77.8832	328	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_003952465.1	s__Mesorhizobium sp003952465	77.5675	385	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
--------------------------------------------------------------------------------
[2023-03-17 09:35:20,137] [INFO] GTDB search result was written to OceanDNA-b26864/result_gtdb.tsv
[2023-03-17 09:35:20,137] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:35:20,139] [INFO] DFAST_QC result json was written to OceanDNA-b26864/dqc_result.json
[2023-03-17 09:35:20,139] [INFO] DFAST_QC completed!
[2023-03-17 09:35:20,139] [INFO] Total running time: 0h2m10s