[2023-03-16 07:49:28,804] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:28,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:28,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference
[2023-03-16 07:49:29,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:29,913] [INFO] Task started: Prodigal
[2023-03-16 07:49:29,913] [INFO] Running command: cat /var/lib/cwl/stgf962f050-afef-4c9d-82ff-a5d6730b2942/OceanDNA-b26841.fa | prodigal -d OceanDNA-b26841/cds.fna -a OceanDNA-b26841/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:56,878] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:56,878] [INFO] Task started: HMMsearch
[2023-03-16 07:49:56,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b26841/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference/reference_markers.hmm OceanDNA-b26841/protein.faa > /dev/null
[2023-03-16 07:49:57,090] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:57,090] [INFO] Found 6/6 markers.
[2023-03-16 07:49:57,135] [INFO] Query marker FASTA was written to OceanDNA-b26841/markers.fasta
[2023-03-16 07:49:57,136] [INFO] Task started: Blastn
[2023-03-16 07:49:57,136] [INFO] Running command: blastn -query OceanDNA-b26841/markers.fasta -db /var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference/reference_markers.fasta -out OceanDNA-b26841/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:58,117] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:58,121] [INFO] Selected 11 target genomes.
[2023-03-16 07:49:58,121] [INFO] Target genome list was writen to OceanDNA-b26841/target_genomes.txt
[2023-03-16 07:49:58,130] [INFO] Task started: fastANI
[2023-03-16 07:49:58,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgf962f050-afef-4c9d-82ff-a5d6730b2942/OceanDNA-b26841.fa --refList OceanDNA-b26841/target_genomes.txt --output OceanDNA-b26841/fastani_result.tsv --threads 1
[2023-03-16 07:50:09,828] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:09,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:50:09,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:50:09,837] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 07:50:09,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 07:50:09,837] [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 alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	97.9471	1352	1412	95	conclusive
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	82.4072	917	1412	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	81.7207	890	1412	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.9971	790	1412	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.6665	667	1412	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	78.2642	375	1412	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.1026	423	1412	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.0214	403	1412	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.9194	358	1412	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.6867	291	1412	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.9222	204	1412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:50:09,839] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26841/tc_result.tsv
[2023-03-16 07:50:09,840] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:50:09,840] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:50:09,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference/checkm_data
[2023-03-16 07:50:09,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:50:09,850] [INFO] Task started: CheckM
[2023-03-16 07:50:09,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26841/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26841/checkm_input OceanDNA-b26841/checkm_result
[2023-03-16 07:51:18,932] [INFO] Task succeeded: CheckM
[2023-03-16 07:51:18,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:51:18,941] [INFO] ===== Completeness check finished =====
[2023-03-16 07:51:18,941] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:51:18,942] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26841/markers.fasta)
[2023-03-16 07:51:18,942] [INFO] Task started: Blastn
[2023-03-16 07:51:18,942] [INFO] Running command: blastn -query OceanDNA-b26841/markers.fasta -db /var/lib/cwl/stgc7c9a765-aa49-442f-9b32-11ce71e21757/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26841/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:51:20,935] [INFO] Task succeeded: Blastn
[2023-03-16 07:51:20,947] [INFO] Selected 11 target genomes.
[2023-03-16 07:51:20,947] [INFO] Target genome list was writen to OceanDNA-b26841/target_genomes_gtdb.txt
[2023-03-16 07:51:21,161] [INFO] Task started: fastANI
[2023-03-16 07:51:21,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgf962f050-afef-4c9d-82ff-a5d6730b2942/OceanDNA-b26841.fa --refList OceanDNA-b26841/target_genomes_gtdb.txt --output OceanDNA-b26841/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:51:32,568] [INFO] Task succeeded: fastANI
[2023-03-16 07:51:32,575] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:51:32,575] [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_902498795.1	s__Hoeflea sp902498795	98.9022	1345	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	conclusive
GCA_018829385.1	s__Hoeflea sp018829385	86.1915	668	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	83.5683	1005	1412	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	82.5915	926	1412	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	82.4072	917	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	82.3126	876	1412	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	82.2482	927	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCA_000961635.1	s__Hoeflea sp000961635	81.9212	595	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	81.7289	889	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001011155.1	s__Hoeflea sp001011155	81.1771	843	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154705.2	s__Hoeflea phototrophica	80.997	790	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:51:32,577] [INFO] GTDB search result was written to OceanDNA-b26841/result_gtdb.tsv
[2023-03-16 07:51:32,579] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:51:32,582] [INFO] DFAST_QC result json was written to OceanDNA-b26841/dqc_result.json
[2023-03-16 07:51:32,582] [INFO] DFAST_QC completed!
[2023-03-16 07:51:32,582] [INFO] Total running time: 0h2m4s