[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference
[2023-03-18 20:59:45,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,683] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,683] [INFO] Running command: cat /var/lib/cwl/stgea49b296-9912-4c63-9056-088afda298f4/OceanDNA-b42824.fa | prodigal -d OceanDNA-b42824/cds.fna -a OceanDNA-b42824/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:00:06,595] [INFO] Task succeeded: Prodigal
[2023-03-18 21:00:06,596] [INFO] Task started: HMMsearch
[2023-03-18 21:00:06,596] [INFO] Running command: hmmsearch --tblout OceanDNA-b42824/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference/reference_markers.hmm OceanDNA-b42824/protein.faa > /dev/null
[2023-03-18 21:00:06,828] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:00:06,829] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgea49b296-9912-4c63-9056-088afda298f4/OceanDNA-b42824.fa]
[2023-03-18 21:00:06,854] [INFO] Query marker FASTA was written to OceanDNA-b42824/markers.fasta
[2023-03-18 21:00:06,855] [INFO] Task started: Blastn
[2023-03-18 21:00:06,855] [INFO] Running command: blastn -query OceanDNA-b42824/markers.fasta -db /var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference/reference_markers.fasta -out OceanDNA-b42824/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:07,451] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:07,451] [INFO] Selected 35 target genomes.
[2023-03-18 21:00:07,452] [INFO] Target genome list was writen to OceanDNA-b42824/target_genomes.txt
[2023-03-18 21:00:07,482] [INFO] Task started: fastANI
[2023-03-18 21:00:07,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgea49b296-9912-4c63-9056-088afda298f4/OceanDNA-b42824.fa --refList OceanDNA-b42824/target_genomes.txt --output OceanDNA-b42824/fastani_result.tsv --threads 1
[2023-03-18 21:00:27,008] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:27,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:27,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:27,013] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:27,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:27,013] [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
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	75.8102	50	1101	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	75.5394	50	1101	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:27,024] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42824/tc_result.tsv
[2023-03-18 21:00:27,025] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:27,025] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:27,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference/checkm_data
[2023-03-18 21:00:27,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:27,046] [INFO] Task started: CheckM
[2023-03-18 21:00:27,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42824/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42824/checkm_input OceanDNA-b42824/checkm_result
[2023-03-18 21:01:20,300] [INFO] Task succeeded: CheckM
[2023-03-18 21:01:20,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.08%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-18 21:01:20,311] [INFO] ===== Completeness check finished =====
[2023-03-18 21:01:20,311] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:01:20,311] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42824/markers.fasta)
[2023-03-18 21:01:20,312] [INFO] Task started: Blastn
[2023-03-18 21:01:20,312] [INFO] Running command: blastn -query OceanDNA-b42824/markers.fasta -db /var/lib/cwl/stg810f68dc-8497-4d9d-9ab2-1b82510fe946/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42824/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:01:21,121] [INFO] Task succeeded: Blastn
[2023-03-18 21:01:21,134] [INFO] Selected 35 target genomes.
[2023-03-18 21:01:21,134] [INFO] Target genome list was writen to OceanDNA-b42824/target_genomes_gtdb.txt
[2023-03-18 21:01:21,170] [INFO] Task started: fastANI
[2023-03-18 21:01:21,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgea49b296-9912-4c63-9056-088afda298f4/OceanDNA-b42824.fa --refList OceanDNA-b42824/target_genomes_gtdb.txt --output OceanDNA-b42824/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:40,280] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:40,284] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:40,284] [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_001447805.1	s__Tenderia electrophaga	76.102	118	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Tenderiales;f__Tenderiaceae;g__Tenderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337735.1	s__Thioalbus denitrificans	76.022	66	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	75.9223	80	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389885.1	s__JABBTK01 sp011389885	75.7271	50	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JABBTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389995.1	s__JAABTG01 sp011389995	75.4697	51	1101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAABTG01;f__JAABTG01;g__JAABTG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:40,285] [INFO] GTDB search result was written to OceanDNA-b42824/result_gtdb.tsv
[2023-03-18 21:01:40,286] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:40,287] [INFO] DFAST_QC result json was written to OceanDNA-b42824/dqc_result.json
[2023-03-18 21:01:40,287] [INFO] DFAST_QC completed!
[2023-03-18 21:01:40,287] [INFO] Total running time: 0h1m56s