[2023-03-15 21:24:36,497] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,497] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,497] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference
[2023-03-15 21:24:37,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,602] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,602] [INFO] Running command: cat /var/lib/cwl/stgcff40376-4921-41a2-8f90-9fc1c286b656/OceanDNA-b26835.fa | prodigal -d OceanDNA-b26835/cds.fna -a OceanDNA-b26835/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:25:06,805] [INFO] Task succeeded: Prodigal
[2023-03-15 21:25:06,805] [INFO] Task started: HMMsearch
[2023-03-15 21:25:06,805] [INFO] Running command: hmmsearch --tblout OceanDNA-b26835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference/reference_markers.hmm OceanDNA-b26835/protein.faa > /dev/null
[2023-03-15 21:25:07,033] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:25:07,034] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcff40376-4921-41a2-8f90-9fc1c286b656/OceanDNA-b26835.fa]
[2023-03-15 21:25:07,062] [INFO] Query marker FASTA was written to OceanDNA-b26835/markers.fasta
[2023-03-15 21:25:07,064] [INFO] Task started: Blastn
[2023-03-15 21:25:07,064] [INFO] Running command: blastn -query OceanDNA-b26835/markers.fasta -db /var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference/reference_markers.fasta -out OceanDNA-b26835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:08,058] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:08,058] [INFO] Selected 10 target genomes.
[2023-03-15 21:25:08,059] [INFO] Target genome list was writen to OceanDNA-b26835/target_genomes.txt
[2023-03-15 21:25:08,064] [INFO] Task started: fastANI
[2023-03-15 21:25:08,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff40376-4921-41a2-8f90-9fc1c286b656/OceanDNA-b26835.fa --refList OceanDNA-b26835/target_genomes.txt --output OceanDNA-b26835/fastani_result.tsv --threads 1
[2023-03-15 21:25:18,663] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:18,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:18,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:18,671] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:25:18,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:25:18,671] [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	85.4237	1086	1562	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	82.4521	983	1562	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	81.6138	889	1562	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	81.4821	860	1562	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.729	786	1562	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.2983	589	1562	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	78.9691	588	1562	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.6922	613	1562	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	78.62	496	1562	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.559	505	1562	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:25:18,671] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26835/tc_result.tsv
[2023-03-15 21:25:18,671] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:18,672] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:18,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference/checkm_data
[2023-03-15 21:25:18,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:18,782] [INFO] Task started: CheckM
[2023-03-15 21:25:18,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26835/checkm_input OceanDNA-b26835/checkm_result
[2023-03-15 21:26:32,527] [INFO] Task succeeded: CheckM
[2023-03-15 21:26:32,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:26:32,531] [INFO] ===== Completeness check finished =====
[2023-03-15 21:26:32,531] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:26:32,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26835/markers.fasta)
[2023-03-15 21:26:32,532] [INFO] Task started: Blastn
[2023-03-15 21:26:32,532] [INFO] Running command: blastn -query OceanDNA-b26835/markers.fasta -db /var/lib/cwl/stgc2210425-5ddb-439b-81bf-e0ccf99d1d41/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:26:34,627] [INFO] Task succeeded: Blastn
[2023-03-15 21:26:34,628] [INFO] Selected 8 target genomes.
[2023-03-15 21:26:34,628] [INFO] Target genome list was writen to OceanDNA-b26835/target_genomes_gtdb.txt
[2023-03-15 21:26:34,777] [INFO] Task started: fastANI
[2023-03-15 21:26:34,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff40376-4921-41a2-8f90-9fc1c286b656/OceanDNA-b26835.fa --refList OceanDNA-b26835/target_genomes_gtdb.txt --output OceanDNA-b26835/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:26:44,292] [INFO] Task succeeded: fastANI
[2023-03-15 21:26:44,297] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:26:44,297] [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_000759435.1	s__Hoeflea sp000759435	92.0504	1196	1562	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	86.5072	1105	1562	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	86.1543	1105	1562	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	85.4136	1087	1562	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	83.8309	671	1562	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	83.5533	610	1562	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	82.5382	953	1562	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	82.4327	975	1562	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:26:44,297] [INFO] GTDB search result was written to OceanDNA-b26835/result_gtdb.tsv
[2023-03-15 21:26:44,298] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:26:44,299] [INFO] DFAST_QC result json was written to OceanDNA-b26835/dqc_result.json
[2023-03-15 21:26:44,299] [INFO] DFAST_QC completed!
[2023-03-15 21:26:44,299] [INFO] Total running time: 0h2m8s