[2023-03-18 23:07:35,847] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:07:35,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:07:35,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference
[2023-03-18 23:07:36,983] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:07:36,983] [INFO] Task started: Prodigal
[2023-03-18 23:07:36,983] [INFO] Running command: cat /var/lib/cwl/stgb3c1f975-b8a7-4754-9a40-8d46f49014a5/OceanDNA-b28636.fa | prodigal -d OceanDNA-b28636/cds.fna -a OceanDNA-b28636/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:07:46,865] [INFO] Task succeeded: Prodigal
[2023-03-18 23:07:46,866] [INFO] Task started: HMMsearch
[2023-03-18 23:07:46,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b28636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference/reference_markers.hmm OceanDNA-b28636/protein.faa > /dev/null
[2023-03-18 23:07:47,041] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:07:47,042] [INFO] Found 6/6 markers.
[2023-03-18 23:07:47,067] [INFO] Query marker FASTA was written to OceanDNA-b28636/markers.fasta
[2023-03-18 23:07:47,068] [INFO] Task started: Blastn
[2023-03-18 23:07:47,068] [INFO] Running command: blastn -query OceanDNA-b28636/markers.fasta -db /var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference/reference_markers.fasta -out OceanDNA-b28636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:07:47,704] [INFO] Task succeeded: Blastn
[2023-03-18 23:07:47,709] [INFO] Selected 34 target genomes.
[2023-03-18 23:07:47,710] [INFO] Target genome list was writen to OceanDNA-b28636/target_genomes.txt
[2023-03-18 23:07:47,731] [INFO] Task started: fastANI
[2023-03-18 23:07:47,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3c1f975-b8a7-4754-9a40-8d46f49014a5/OceanDNA-b28636.fa --refList OceanDNA-b28636/target_genomes.txt --output OceanDNA-b28636/fastani_result.tsv --threads 1
[2023-03-18 23:08:06,871] [INFO] Task succeeded: fastANI
[2023-03-18 23:08:06,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:08:06,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:08:06,874] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:08:06,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:08:06,875] [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
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.3466	56	484	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:08:06,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28636/tc_result.tsv
[2023-03-18 23:08:06,877] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:08:06,877] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:08:06,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference/checkm_data
[2023-03-18 23:08:06,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:08:06,883] [INFO] Task started: CheckM
[2023-03-18 23:08:06,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28636/checkm_input OceanDNA-b28636/checkm_result
[2023-03-18 23:08:36,251] [INFO] Task succeeded: CheckM
[2023-03-18 23:08:36,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:08:36,275] [INFO] ===== Completeness check finished =====
[2023-03-18 23:08:36,275] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:08:36,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28636/markers.fasta)
[2023-03-18 23:08:36,276] [INFO] Task started: Blastn
[2023-03-18 23:08:36,276] [INFO] Running command: blastn -query OceanDNA-b28636/markers.fasta -db /var/lib/cwl/stg7e95a33b-86b9-4526-8880-c1b63cc33e89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:08:37,373] [INFO] Task succeeded: Blastn
[2023-03-18 23:08:37,379] [INFO] Selected 21 target genomes.
[2023-03-18 23:08:37,379] [INFO] Target genome list was writen to OceanDNA-b28636/target_genomes_gtdb.txt
[2023-03-18 23:08:37,434] [INFO] Task started: fastANI
[2023-03-18 23:08:37,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3c1f975-b8a7-4754-9a40-8d46f49014a5/OceanDNA-b28636.fa --refList OceanDNA-b28636/target_genomes_gtdb.txt --output OceanDNA-b28636/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:08:48,872] [INFO] Task succeeded: fastANI
[2023-03-18 23:08:48,876] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:08:48,877] [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_902525995.1	s__CABZJG01 sp902525995	96.9986	233	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002726375.1	s__CABZJG01 sp002726375	87.7065	308	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	-
GCA_902512685.1	s__CABZJG01 sp902512685	85.9563	269	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.75	97.42	0.59	0.54	7	-
GCA_001642945.1	s__LGRT01 sp001642945	78.3028	62	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
GCA_016778765.1	s__LGRT01 sp016778765	77.1435	57	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	98.26	96.00	0.81	0.61	8	-
--------------------------------------------------------------------------------
[2023-03-18 23:08:48,877] [INFO] GTDB search result was written to OceanDNA-b28636/result_gtdb.tsv
[2023-03-18 23:08:48,877] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:08:48,878] [INFO] DFAST_QC result json was written to OceanDNA-b28636/dqc_result.json
[2023-03-18 23:08:48,878] [INFO] DFAST_QC completed!
[2023-03-18 23:08:48,879] [INFO] Total running time: 0h1m13s