[2023-03-16 12:37:45,857] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:45,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:45,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference
[2023-03-16 12:37:48,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:48,637] [INFO] Task started: Prodigal
[2023-03-16 12:37:48,637] [INFO] Running command: cat /var/lib/cwl/stgda161f00-3454-4ec4-b6f2-3ee0312b9261/OceanDNA-b10765.fa | prodigal -d OceanDNA-b10765/cds.fna -a OceanDNA-b10765/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:37:56,831] [INFO] Task succeeded: Prodigal
[2023-03-16 12:37:56,831] [INFO] Task started: HMMsearch
[2023-03-16 12:37:56,831] [INFO] Running command: hmmsearch --tblout OceanDNA-b10765/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference/reference_markers.hmm OceanDNA-b10765/protein.faa > /dev/null
[2023-03-16 12:37:57,020] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:37:57,021] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda161f00-3454-4ec4-b6f2-3ee0312b9261/OceanDNA-b10765.fa]
[2023-03-16 12:37:57,029] [INFO] Query marker FASTA was written to OceanDNA-b10765/markers.fasta
[2023-03-16 12:37:57,029] [INFO] Task started: Blastn
[2023-03-16 12:37:57,029] [INFO] Running command: blastn -query OceanDNA-b10765/markers.fasta -db /var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference/reference_markers.fasta -out OceanDNA-b10765/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:37:57,895] [INFO] Task succeeded: Blastn
[2023-03-16 12:37:57,895] [INFO] Selected 32 target genomes.
[2023-03-16 12:37:57,896] [INFO] Target genome list was writen to OceanDNA-b10765/target_genomes.txt
[2023-03-16 12:37:57,913] [INFO] Task started: fastANI
[2023-03-16 12:37:57,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgda161f00-3454-4ec4-b6f2-3ee0312b9261/OceanDNA-b10765.fa --refList OceanDNA-b10765/target_genomes.txt --output OceanDNA-b10765/fastani_result.tsv --threads 1
[2023-03-16 12:38:15,762] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:15,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:15,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:15,763] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:15,763] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:38:15,763] [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
--------------------------------------------------------------------------------
[2023-03-16 12:38:15,763] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10765/tc_result.tsv
[2023-03-16 12:38:15,763] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:15,763] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:15,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference/checkm_data
[2023-03-16 12:38:15,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:15,769] [INFO] Task started: CheckM
[2023-03-16 12:38:15,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10765/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10765/checkm_input OceanDNA-b10765/checkm_result
[2023-03-16 12:38:40,911] [INFO] Task succeeded: CheckM
[2023-03-16 12:38:40,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.11%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:38:40,913] [INFO] ===== Completeness check finished =====
[2023-03-16 12:38:40,914] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:38:40,914] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10765/markers.fasta)
[2023-03-16 12:38:40,915] [INFO] Task started: Blastn
[2023-03-16 12:38:40,915] [INFO] Running command: blastn -query OceanDNA-b10765/markers.fasta -db /var/lib/cwl/stgdfd0d6c2-2a6e-4b72-b459-64702b8a9a62/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10765/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:42,385] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:42,386] [INFO] Selected 15 target genomes.
[2023-03-16 12:38:42,386] [INFO] Target genome list was writen to OceanDNA-b10765/target_genomes_gtdb.txt
[2023-03-16 12:38:42,708] [INFO] Task started: fastANI
[2023-03-16 12:38:42,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgda161f00-3454-4ec4-b6f2-3ee0312b9261/OceanDNA-b10765.fa --refList OceanDNA-b10765/target_genomes_gtdb.txt --output OceanDNA-b10765/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:38:48,589] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:48,594] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:38:48,594] [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_002723075.1	s__UBA724 sp002723075	84.9762	112	138	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.07	97.94	0.92	0.77	6	-
GCA_002171575.2	s__UBA724 sp002171575	83.7028	98	138	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536935.1	s__UBA724 sp902536935	82.6699	95	138	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	96.07	96.07	0.80	0.80	2	-
GCA_902619855.1	s__UBA724 sp902619855	79.2571	69	138	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586905.1	s__UBA724 sp902586905	78.9365	67	138	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430545.1	s__UBA724 sp002430545	78.4842	69	138	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 12:38:48,595] [INFO] GTDB search result was written to OceanDNA-b10765/result_gtdb.tsv
[2023-03-16 12:38:48,595] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:38:48,595] [INFO] DFAST_QC result json was written to OceanDNA-b10765/dqc_result.json
[2023-03-16 12:38:48,596] [INFO] DFAST_QC completed!
[2023-03-16 12:38:48,596] [INFO] Total running time: 0h1m3s