[2023-03-15 07:03:38,915] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,916] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference
[2023-03-15 07:03:40,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:40,128] [INFO] Task started: Prodigal
[2023-03-15 07:03:40,128] [INFO] Running command: cat /var/lib/cwl/stgae27f8c3-969b-4cbf-80d8-5400adae889a/OceanDNA-b26843.fa | prodigal -d OceanDNA-b26843/cds.fna -a OceanDNA-b26843/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:04:06,035] [INFO] Task succeeded: Prodigal
[2023-03-15 07:04:06,036] [INFO] Task started: HMMsearch
[2023-03-15 07:04:06,036] [INFO] Running command: hmmsearch --tblout OceanDNA-b26843/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference/reference_markers.hmm OceanDNA-b26843/protein.faa > /dev/null
[2023-03-15 07:04:06,258] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:04:06,259] [INFO] Found 6/6 markers.
[2023-03-15 07:04:06,321] [INFO] Query marker FASTA was written to OceanDNA-b26843/markers.fasta
[2023-03-15 07:04:06,321] [INFO] Task started: Blastn
[2023-03-15 07:04:06,321] [INFO] Running command: blastn -query OceanDNA-b26843/markers.fasta -db /var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference/reference_markers.fasta -out OceanDNA-b26843/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:07,180] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:07,185] [INFO] Selected 9 target genomes.
[2023-03-15 07:04:07,186] [INFO] Target genome list was writen to OceanDNA-b26843/target_genomes.txt
[2023-03-15 07:04:07,191] [INFO] Task started: fastANI
[2023-03-15 07:04:07,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgae27f8c3-969b-4cbf-80d8-5400adae889a/OceanDNA-b26843.fa --refList OceanDNA-b26843/target_genomes.txt --output OceanDNA-b26843/fastani_result.tsv --threads 1
[2023-03-15 07:04:16,505] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:16,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:16,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:16,513] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:16,513] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:04:16,513] [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 halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	82.7982	927	1352	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	82.4156	948	1352	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	80.9802	787	1352	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.5884	696	1352	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.3403	633	1352	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.5375	358	1352	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.4299	305	1352	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	77.2905	243	1352	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	77.2851	292	1352	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:04:16,514] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26843/tc_result.tsv
[2023-03-15 07:04:16,516] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:16,516] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:16,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference/checkm_data
[2023-03-15 07:04:16,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:16,528] [INFO] Task started: CheckM
[2023-03-15 07:04:16,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26843/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26843/checkm_input OceanDNA-b26843/checkm_result
[2023-03-15 07:05:21,330] [INFO] Task succeeded: CheckM
[2023-03-15 07:05:21,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:05:21,340] [INFO] ===== Completeness check finished =====
[2023-03-15 07:05:21,340] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:05:21,340] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26843/markers.fasta)
[2023-03-15 07:05:21,341] [INFO] Task started: Blastn
[2023-03-15 07:05:21,342] [INFO] Running command: blastn -query OceanDNA-b26843/markers.fasta -db /var/lib/cwl/stg9a2f9eca-bb25-46b4-b23a-ea88edc34e3b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26843/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:05:22,878] [INFO] Task succeeded: Blastn
[2023-03-15 07:05:22,886] [INFO] Selected 11 target genomes.
[2023-03-15 07:05:22,886] [INFO] Target genome list was writen to OceanDNA-b26843/target_genomes_gtdb.txt
[2023-03-15 07:05:23,041] [INFO] Task started: fastANI
[2023-03-15 07:05:23,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgae27f8c3-969b-4cbf-80d8-5400adae889a/OceanDNA-b26843.fa --refList OceanDNA-b26843/target_genomes_gtdb.txt --output OceanDNA-b26843/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:05:33,941] [INFO] Task succeeded: fastANI
[2023-03-15 07:05:33,949] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:05:33,949] [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_002733955.1	s__Hoeflea sp002733955	84.3166	1023	1352	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	83.0909	585	1352	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	82.7999	926	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	82.4364	927	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCA_000961635.1	s__Hoeflea sp000961635	81.9504	572	1352	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	81.8014	874	1352	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	81.7183	847	1352	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	81.6605	840	1352	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	81.5562	889	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_001703635.1	s__Hoeflea olei	80.9802	787	1352	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	80.5797	697	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:05:33,952] [INFO] GTDB search result was written to OceanDNA-b26843/result_gtdb.tsv
[2023-03-15 07:05:33,958] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:05:33,963] [INFO] DFAST_QC result json was written to OceanDNA-b26843/dqc_result.json
[2023-03-15 07:05:33,963] [INFO] DFAST_QC completed!
[2023-03-15 07:05:33,963] [INFO] Total running time: 0h1m55s