[2023-03-15 21:01:44,355] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,355] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference
[2023-03-15 21:01:45,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stgdf575cc4-7ab3-4689-85ab-d73d74845ce7/OceanDNA-b37653.fa | prodigal -d OceanDNA-b37653/cds.fna -a OceanDNA-b37653/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:04,083] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:04,084] [INFO] Task started: HMMsearch
[2023-03-15 21:02:04,084] [INFO] Running command: hmmsearch --tblout OceanDNA-b37653/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference/reference_markers.hmm OceanDNA-b37653/protein.faa > /dev/null
[2023-03-15 21:02:04,293] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:04,293] [INFO] Found 6/6 markers.
[2023-03-15 21:02:04,311] [INFO] Query marker FASTA was written to OceanDNA-b37653/markers.fasta
[2023-03-15 21:02:04,312] [INFO] Task started: Blastn
[2023-03-15 21:02:04,312] [INFO] Running command: blastn -query OceanDNA-b37653/markers.fasta -db /var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference/reference_markers.fasta -out OceanDNA-b37653/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:04,901] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:04,902] [INFO] Selected 25 target genomes.
[2023-03-15 21:02:04,902] [INFO] Target genome list was writen to OceanDNA-b37653/target_genomes.txt
[2023-03-15 21:02:04,920] [INFO] Task started: fastANI
[2023-03-15 21:02:04,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf575cc4-7ab3-4689-85ab-d73d74845ce7/OceanDNA-b37653.fa --refList OceanDNA-b37653/target_genomes.txt --output OceanDNA-b37653/fastani_result.tsv --threads 1
[2023-03-15 21:02:20,361] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:20,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:20,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:20,364] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:20,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:20,364] [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
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.1389	51	1032	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.0324	52	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:20,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37653/tc_result.tsv
[2023-03-15 21:02:20,365] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:20,365] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:20,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference/checkm_data
[2023-03-15 21:02:20,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:20,372] [INFO] Task started: CheckM
[2023-03-15 21:02:20,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37653/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37653/checkm_input OceanDNA-b37653/checkm_result
[2023-03-15 21:03:07,730] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:07,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:07,734] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:07,734] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:07,734] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37653/markers.fasta)
[2023-03-15 21:03:07,736] [INFO] Task started: Blastn
[2023-03-15 21:03:07,736] [INFO] Running command: blastn -query OceanDNA-b37653/markers.fasta -db /var/lib/cwl/stg53cd3b43-481f-43ed-aba6-dd9dfce5354a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37653/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:08,713] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:08,714] [INFO] Selected 20 target genomes.
[2023-03-15 21:03:08,714] [INFO] Target genome list was writen to OceanDNA-b37653/target_genomes_gtdb.txt
[2023-03-15 21:03:09,321] [INFO] Task started: fastANI
[2023-03-15 21:03:09,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf575cc4-7ab3-4689-85ab-d73d74845ce7/OceanDNA-b37653.fa --refList OceanDNA-b37653/target_genomes_gtdb.txt --output OceanDNA-b37653/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:21,289] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:21,294] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:21,295] [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_002862465.1	s__Halioglobus sp002862465	79.5867	570	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862985.1	s__Halioglobus sp002862985	77.5859	136	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.7649	134	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	76.5502	103	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCA_003646415.1	s__Halioglobus sp003646415	76.3213	51	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	76.1426	55	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	76.1389	51	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.0324	52	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:21,295] [INFO] GTDB search result was written to OceanDNA-b37653/result_gtdb.tsv
[2023-03-15 21:03:21,295] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:21,296] [INFO] DFAST_QC result json was written to OceanDNA-b37653/dqc_result.json
[2023-03-15 21:03:21,296] [INFO] DFAST_QC completed!
[2023-03-15 21:03:21,296] [INFO] Total running time: 0h1m37s