[2023-03-18 08:17:17,674] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,674] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference
[2023-03-18 08:17:18,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg22045f70-ef86-40cb-a612-3428516cc8c6/OceanDNA-b25795.fa | prodigal -d OceanDNA-b25795/cds.fna -a OceanDNA-b25795/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:22,379] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:22,379] [INFO] Task started: HMMsearch
[2023-03-18 08:17:22,379] [INFO] Running command: hmmsearch --tblout OceanDNA-b25795/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference/reference_markers.hmm OceanDNA-b25795/protein.faa > /dev/null
[2023-03-18 08:17:22,507] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:22,508] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg22045f70-ef86-40cb-a612-3428516cc8c6/OceanDNA-b25795.fa]
[2023-03-18 08:17:22,514] [INFO] Query marker FASTA was written to OceanDNA-b25795/markers.fasta
[2023-03-18 08:17:22,514] [INFO] Task started: Blastn
[2023-03-18 08:17:22,514] [INFO] Running command: blastn -query OceanDNA-b25795/markers.fasta -db /var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference/reference_markers.fasta -out OceanDNA-b25795/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:22,986] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:22,986] [INFO] Selected 6 target genomes.
[2023-03-18 08:17:22,987] [INFO] Target genome list was writen to OceanDNA-b25795/target_genomes.txt
[2023-03-18 08:17:22,990] [INFO] Task started: fastANI
[2023-03-18 08:17:22,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg22045f70-ef86-40cb-a612-3428516cc8c6/OceanDNA-b25795.fa --refList OceanDNA-b25795/target_genomes.txt --output OceanDNA-b25795/fastani_result.tsv --threads 1
[2023-03-18 08:17:24,508] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:24,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:24,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:24,559] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:24,560] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:24,560] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	78.7866	104	171	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:24,560] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25795/tc_result.tsv
[2023-03-18 08:17:24,560] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:24,560] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:24,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference/checkm_data
[2023-03-18 08:17:24,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:24,563] [INFO] Task started: CheckM
[2023-03-18 08:17:24,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25795/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25795/checkm_input OceanDNA-b25795/checkm_result
[2023-03-18 08:17:42,356] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:42,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:17:42,358] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:42,358] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:42,358] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25795/markers.fasta)
[2023-03-18 08:17:42,360] [INFO] Task started: Blastn
[2023-03-18 08:17:42,360] [INFO] Running command: blastn -query OceanDNA-b25795/markers.fasta -db /var/lib/cwl/stgae2c23bc-0713-453b-9503-af317c7efa42/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25795/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:43,407] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:43,408] [INFO] Selected 10 target genomes.
[2023-03-18 08:17:43,408] [INFO] Target genome list was writen to OceanDNA-b25795/target_genomes_gtdb.txt
[2023-03-18 08:17:43,423] [INFO] Task started: fastANI
[2023-03-18 08:17:43,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg22045f70-ef86-40cb-a612-3428516cc8c6/OceanDNA-b25795.fa --refList OceanDNA-b25795/target_genomes_gtdb.txt --output OceanDNA-b25795/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:17:45,673] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:45,680] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:17:45,680] [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_902595745.1	s__Pelagibacter sp902595745	95.3406	94	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902558795.1	s__Pelagibacter sp902558795	87.1988	87	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880265.1	s__Pelagibacter sp017880265	86.0798	110	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.65	97.65	0.82	0.82	2	-
GCF_000472565.1	s__Pelagibacter ubique_C	85.7931	156	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279685.1	s__Pelagibacter sp003279685	85.1021	146	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902511185.1	s__Pelagibacter sp902511185	85.0898	95	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653385.1	s__Pelagibacter sp014653385	84.9465	127	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.45	95.45	0.77	0.77	2	-
GCA_902556905.1	s__Pelagibacter sp902556905	84.5831	133	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279715.1	s__Pelagibacter sp003279715	84.3835	136	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902513955.1	s__Pelagibacter sp902513955	83.3449	128	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:17:45,681] [INFO] GTDB search result was written to OceanDNA-b25795/result_gtdb.tsv
[2023-03-18 08:17:45,681] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:17:45,682] [INFO] DFAST_QC result json was written to OceanDNA-b25795/dqc_result.json
[2023-03-18 08:17:45,682] [INFO] DFAST_QC completed!
[2023-03-18 08:17:45,682] [INFO] Total running time: 0h0m28s