[2023-03-15 21:01:46,256] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:46,256] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:46,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference
[2023-03-15 21:01:47,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:47,361] [INFO] Task started: Prodigal
[2023-03-15 21:01:47,361] [INFO] Running command: cat /var/lib/cwl/stg0cedd4b6-40e0-4a40-b304-4b96cdf70043/OceanDNA-b26870.fa | prodigal -d OceanDNA-b26870/cds.fna -a OceanDNA-b26870/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:15,523] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:15,523] [INFO] Task started: HMMsearch
[2023-03-15 21:02:15,523] [INFO] Running command: hmmsearch --tblout OceanDNA-b26870/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference/reference_markers.hmm OceanDNA-b26870/protein.faa > /dev/null
[2023-03-15 21:02:15,736] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:15,736] [INFO] Found 6/6 markers.
[2023-03-15 21:02:15,762] [INFO] Query marker FASTA was written to OceanDNA-b26870/markers.fasta
[2023-03-15 21:02:15,762] [INFO] Task started: Blastn
[2023-03-15 21:02:15,762] [INFO] Running command: blastn -query OceanDNA-b26870/markers.fasta -db /var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference/reference_markers.fasta -out OceanDNA-b26870/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:16,728] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:16,729] [INFO] Selected 10 target genomes.
[2023-03-15 21:02:16,729] [INFO] Target genome list was writen to OceanDNA-b26870/target_genomes.txt
[2023-03-15 21:02:16,735] [INFO] Task started: fastANI
[2023-03-15 21:02:16,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cedd4b6-40e0-4a40-b304-4b96cdf70043/OceanDNA-b26870.fa --refList OceanDNA-b26870/target_genomes.txt --output OceanDNA-b26870/fastani_result.tsv --threads 1
[2023-03-15 21:02:27,405] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:27,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:27,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:27,412] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:27,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:27,413] [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	87.6432	1142	1466	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	83.683	1124	1466	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	81.8973	943	1466	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.8641	848	1466	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	80.0659	712	1466	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.2916	433	1466	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	78.2089	410	1466	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.0835	474	1466	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	78.0208	388	1466	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.7759	407	1466	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:27,413] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26870/tc_result.tsv
[2023-03-15 21:02:27,413] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:27,413] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:27,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference/checkm_data
[2023-03-15 21:02:27,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:27,419] [INFO] Task started: CheckM
[2023-03-15 21:02:27,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26870/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26870/checkm_input OceanDNA-b26870/checkm_result
[2023-03-15 21:03:40,507] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:40,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:40,510] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:40,510] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:40,510] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26870/markers.fasta)
[2023-03-15 21:03:40,512] [INFO] Task started: Blastn
[2023-03-15 21:03:40,512] [INFO] Running command: blastn -query OceanDNA-b26870/markers.fasta -db /var/lib/cwl/stg6c14bdd7-c1c0-453e-a47b-5a55cd88cc57/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26870/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:42,511] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:42,512] [INFO] Selected 9 target genomes.
[2023-03-15 21:03:42,512] [INFO] Target genome list was writen to OceanDNA-b26870/target_genomes_gtdb.txt
[2023-03-15 21:03:42,708] [INFO] Task started: fastANI
[2023-03-15 21:03:42,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cedd4b6-40e0-4a40-b304-4b96cdf70043/OceanDNA-b26870.fa --refList OceanDNA-b26870/target_genomes_gtdb.txt --output OceanDNA-b26870/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:52,419] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:52,425] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:52,425] [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	96.9424	1367	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900220985.1	s__Hoeflea halophila	87.6205	1144	1466	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	84.1455	641	1466	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	83.6984	1092	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_000759435.1	s__Hoeflea sp000759435	82.7712	938	1466	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	82.4373	925	1466	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961635.1	s__Hoeflea sp000961635	82.4196	615	1466	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	82.046	962	1466	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	80.8639	848	1466	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 21:03:52,425] [INFO] GTDB search result was written to OceanDNA-b26870/result_gtdb.tsv
[2023-03-15 21:03:52,425] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:52,427] [INFO] DFAST_QC result json was written to OceanDNA-b26870/dqc_result.json
[2023-03-15 21:03:52,427] [INFO] DFAST_QC completed!
[2023-03-15 21:03:52,427] [INFO] Total running time: 0h2m6s