[2023-03-17 13:46:30,402] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:46:30,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:46:30,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference
[2023-03-17 13:46:32,764] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:46:32,777] [INFO] Task started: Prodigal
[2023-03-17 13:46:32,777] [INFO] Running command: cat /var/lib/cwl/stg2be802ea-8390-42e4-8d45-100050f15613/OceanDNA-b26777.fa | prodigal -d OceanDNA-b26777/cds.fna -a OceanDNA-b26777/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:46:38,905] [INFO] Task succeeded: Prodigal
[2023-03-17 13:46:38,905] [INFO] Task started: HMMsearch
[2023-03-17 13:46:38,905] [INFO] Running command: hmmsearch --tblout OceanDNA-b26777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference/reference_markers.hmm OceanDNA-b26777/protein.faa > /dev/null
[2023-03-17 13:46:39,029] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:46:39,029] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2be802ea-8390-42e4-8d45-100050f15613/OceanDNA-b26777.fa]
[2023-03-17 13:46:39,043] [INFO] Query marker FASTA was written to OceanDNA-b26777/markers.fasta
[2023-03-17 13:46:39,043] [INFO] Task started: Blastn
[2023-03-17 13:46:39,043] [INFO] Running command: blastn -query OceanDNA-b26777/markers.fasta -db /var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference/reference_markers.fasta -out OceanDNA-b26777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:46:39,628] [INFO] Task succeeded: Blastn
[2023-03-17 13:46:39,628] [INFO] Selected 17 target genomes.
[2023-03-17 13:46:39,629] [INFO] Target genome list was writen to OceanDNA-b26777/target_genomes.txt
[2023-03-17 13:46:39,637] [INFO] Task started: fastANI
[2023-03-17 13:46:39,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be802ea-8390-42e4-8d45-100050f15613/OceanDNA-b26777.fa --refList OceanDNA-b26777/target_genomes.txt --output OceanDNA-b26777/fastani_result.tsv --threads 1
[2023-03-17 13:46:56,883] [INFO] Task succeeded: fastANI
[2023-03-17 13:46:56,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:46:56,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:46:56,889] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:46:56,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:46:56,889] [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
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.2179	50	175	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.1068	56	175	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	77.0617	51	175	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	77.0148	52	175	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:46:56,889] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26777/tc_result.tsv
[2023-03-17 13:46:56,889] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:46:56,902] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:46:56,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference/checkm_data
[2023-03-17 13:46:56,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:46:56,918] [INFO] Task started: CheckM
[2023-03-17 13:46:56,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26777/checkm_input OceanDNA-b26777/checkm_result
[2023-03-17 13:47:24,772] [INFO] Task succeeded: CheckM
[2023-03-17 13:47:24,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.68%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:47:24,774] [INFO] ===== Completeness check finished =====
[2023-03-17 13:47:24,774] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:47:24,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26777/markers.fasta)
[2023-03-17 13:47:24,775] [INFO] Task started: Blastn
[2023-03-17 13:47:24,775] [INFO] Running command: blastn -query OceanDNA-b26777/markers.fasta -db /var/lib/cwl/stg63a187f6-05ef-4c80-b28b-f38156f554f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:47:25,684] [INFO] Task succeeded: Blastn
[2023-03-17 13:47:25,685] [INFO] Selected 18 target genomes.
[2023-03-17 13:47:25,685] [INFO] Target genome list was writen to OceanDNA-b26777/target_genomes_gtdb.txt
[2023-03-17 13:47:25,845] [INFO] Task started: fastANI
[2023-03-17 13:47:25,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be802ea-8390-42e4-8d45-100050f15613/OceanDNA-b26777.fa --refList OceanDNA-b26777/target_genomes_gtdb.txt --output OceanDNA-b26777/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:47:39,173] [INFO] Task succeeded: fastANI
[2023-03-17 13:47:39,177] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:47:39,177] [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_000300335.1	s__Nitratireductor pacificus	77.1029	52	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	77.0821	56	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	77.0617	51	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 13:47:39,177] [INFO] GTDB search result was written to OceanDNA-b26777/result_gtdb.tsv
[2023-03-17 13:47:39,177] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:47:39,178] [INFO] DFAST_QC result json was written to OceanDNA-b26777/dqc_result.json
[2023-03-17 13:47:39,178] [INFO] DFAST_QC completed!
[2023-03-17 13:47:39,178] [INFO] Total running time: 0h1m9s