[2023-03-16 08:30:41,846] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:30:41,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:30:41,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference
[2023-03-16 08:30:42,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:30:42,956] [INFO] Task started: Prodigal
[2023-03-16 08:30:42,957] [INFO] Running command: cat /var/lib/cwl/stgfa6410a6-ecd0-40b9-88bf-f01ebac9d23e/OceanDNA-b29586.fa | prodigal -d OceanDNA-b29586/cds.fna -a OceanDNA-b29586/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:30:53,594] [INFO] Task succeeded: Prodigal
[2023-03-16 08:30:53,595] [INFO] Task started: HMMsearch
[2023-03-16 08:30:53,595] [INFO] Running command: hmmsearch --tblout OceanDNA-b29586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference/reference_markers.hmm OceanDNA-b29586/protein.faa > /dev/null
[2023-03-16 08:30:53,763] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:30:53,764] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfa6410a6-ecd0-40b9-88bf-f01ebac9d23e/OceanDNA-b29586.fa]
[2023-03-16 08:30:53,787] [INFO] Query marker FASTA was written to OceanDNA-b29586/markers.fasta
[2023-03-16 08:30:53,789] [INFO] Task started: Blastn
[2023-03-16 08:30:53,789] [INFO] Running command: blastn -query OceanDNA-b29586/markers.fasta -db /var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference/reference_markers.fasta -out OceanDNA-b29586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:30:54,241] [INFO] Task succeeded: Blastn
[2023-03-16 08:30:54,246] [INFO] Selected 14 target genomes.
[2023-03-16 08:30:54,246] [INFO] Target genome list was writen to OceanDNA-b29586/target_genomes.txt
[2023-03-16 08:30:54,273] [INFO] Task started: fastANI
[2023-03-16 08:30:54,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6410a6-ecd0-40b9-88bf-f01ebac9d23e/OceanDNA-b29586.fa --refList OceanDNA-b29586/target_genomes.txt --output OceanDNA-b29586/fastani_result.tsv --threads 1
[2023-03-16 08:31:02,192] [INFO] Task succeeded: fastANI
[2023-03-16 08:31:02,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:31:02,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:31:02,199] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:31:02,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:31:02,199] [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
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	78.7934	242	507	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	78.7506	244	507	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	78.494	232	507	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	78.1931	230	507	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.4911	198	507	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	77.3455	211	507	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.3388	86	507	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	76.1636	57	507	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:31:02,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29586/tc_result.tsv
[2023-03-16 08:31:02,201] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:31:02,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:31:02,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference/checkm_data
[2023-03-16 08:31:02,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:31:02,254] [INFO] Task started: CheckM
[2023-03-16 08:31:02,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29586/checkm_input OceanDNA-b29586/checkm_result
[2023-03-16 08:31:33,028] [INFO] Task succeeded: CheckM
[2023-03-16 08:31:33,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:31:33,081] [INFO] ===== Completeness check finished =====
[2023-03-16 08:31:33,081] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:31:33,081] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29586/markers.fasta)
[2023-03-16 08:31:33,082] [INFO] Task started: Blastn
[2023-03-16 08:31:33,082] [INFO] Running command: blastn -query OceanDNA-b29586/markers.fasta -db /var/lib/cwl/stg397d672c-9a78-4691-bfeb-79ceed07fd4c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:31:33,554] [INFO] Task succeeded: Blastn
[2023-03-16 08:31:33,558] [INFO] Selected 10 target genomes.
[2023-03-16 08:31:33,558] [INFO] Target genome list was writen to OceanDNA-b29586/target_genomes_gtdb.txt
[2023-03-16 08:31:33,571] [INFO] Task started: fastANI
[2023-03-16 08:31:33,571] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6410a6-ecd0-40b9-88bf-f01ebac9d23e/OceanDNA-b29586.fa --refList OceanDNA-b29586/target_genomes_gtdb.txt --output OceanDNA-b29586/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:31:39,215] [INFO] Task succeeded: fastANI
[2023-03-16 08:31:39,222] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:31:39,222] [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_018861045.1	s__Octadecabacter sp018861045	78.7996	212	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	78.7934	242	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017886375.1	s__Octadecabacter sp017886375	78.7074	231	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155735.2	s__Octadecabacter arcticus	78.5463	230	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	78.5116	231	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	78.3795	205	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	78.1931	230	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533975.1	s__Octadecabacter sp003533975	78.0256	163	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	77.4911	198	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	76.3388	86	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:31:39,224] [INFO] GTDB search result was written to OceanDNA-b29586/result_gtdb.tsv
[2023-03-16 08:31:39,226] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:31:39,229] [INFO] DFAST_QC result json was written to OceanDNA-b29586/dqc_result.json
[2023-03-16 08:31:39,229] [INFO] DFAST_QC completed!
[2023-03-16 08:31:39,229] [INFO] Total running time: 0h0m57s