[2023-03-16 17:35:01,768] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:35:01,769] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:35:01,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference
[2023-03-16 17:35:06,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:35:06,576] [INFO] Task started: Prodigal
[2023-03-16 17:35:06,576] [INFO] Running command: cat /var/lib/cwl/stg07380c5c-cf8d-4b57-9b0d-38545bc8d722/OceanDNA-b12071.fa | prodigal -d OceanDNA-b12071/cds.fna -a OceanDNA-b12071/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:35:18,944] [INFO] Task succeeded: Prodigal
[2023-03-16 17:35:18,944] [INFO] Task started: HMMsearch
[2023-03-16 17:35:18,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b12071/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference/reference_markers.hmm OceanDNA-b12071/protein.faa > /dev/null
[2023-03-16 17:35:19,108] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:35:19,108] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07380c5c-cf8d-4b57-9b0d-38545bc8d722/OceanDNA-b12071.fa]
[2023-03-16 17:35:19,121] [INFO] Query marker FASTA was written to OceanDNA-b12071/markers.fasta
[2023-03-16 17:35:19,123] [INFO] Task started: Blastn
[2023-03-16 17:35:19,123] [INFO] Running command: blastn -query OceanDNA-b12071/markers.fasta -db /var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference/reference_markers.fasta -out OceanDNA-b12071/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:35:19,943] [INFO] Task succeeded: Blastn
[2023-03-16 17:35:19,944] [INFO] Selected 10 target genomes.
[2023-03-16 17:35:19,944] [INFO] Target genome list was writen to OceanDNA-b12071/target_genomes.txt
[2023-03-16 17:35:19,954] [INFO] Task started: fastANI
[2023-03-16 17:35:19,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg07380c5c-cf8d-4b57-9b0d-38545bc8d722/OceanDNA-b12071.fa --refList OceanDNA-b12071/target_genomes.txt --output OceanDNA-b12071/fastani_result.tsv --threads 1
[2023-03-16 17:35:26,449] [INFO] Task succeeded: fastANI
[2023-03-16 17:35:26,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:35:26,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:35:26,450] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:35:26,450] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:35:26,450] [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 17:35:26,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12071/tc_result.tsv
[2023-03-16 17:35:26,451] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:35:26,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:35:26,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference/checkm_data
[2023-03-16 17:35:26,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:35:26,465] [INFO] Task started: CheckM
[2023-03-16 17:35:26,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12071/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12071/checkm_input OceanDNA-b12071/checkm_result
[2023-03-16 17:36:00,084] [INFO] Task succeeded: CheckM
[2023-03-16 17:36:00,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:36:00,088] [INFO] ===== Completeness check finished =====
[2023-03-16 17:36:00,089] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:36:00,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12071/markers.fasta)
[2023-03-16 17:36:00,091] [INFO] Task started: Blastn
[2023-03-16 17:36:00,091] [INFO] Running command: blastn -query OceanDNA-b12071/markers.fasta -db /var/lib/cwl/stgfeaf1769-2093-4b60-b1a5-bd9852de6477/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12071/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:36:00,735] [INFO] Task succeeded: Blastn
[2023-03-16 17:36:00,737] [INFO] Selected 19 target genomes.
[2023-03-16 17:36:00,737] [INFO] Target genome list was writen to OceanDNA-b12071/target_genomes_gtdb.txt
[2023-03-16 17:36:00,755] [INFO] Task started: fastANI
[2023-03-16 17:36:00,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg07380c5c-cf8d-4b57-9b0d-38545bc8d722/OceanDNA-b12071.fa --refList OceanDNA-b12071/target_genomes_gtdb.txt --output OceanDNA-b12071/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:36:09,842] [INFO] Task succeeded: fastANI
[2023-03-16 17:36:09,846] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:36:09,846] [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_902578505.1	s__UBA974 sp902578505	89.8748	162	320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	98.75	98.75	0.58	0.58	2	-
GCA_002722795.1	s__UBA974 sp002722795	78.6849	141	320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723115.1	s__UBA974 sp002723115	78.3829	132	320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693775.1	s__UBA974 sp002693775	77.858	109	320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:36:09,846] [INFO] GTDB search result was written to OceanDNA-b12071/result_gtdb.tsv
[2023-03-16 17:36:09,846] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:36:09,847] [INFO] DFAST_QC result json was written to OceanDNA-b12071/dqc_result.json
[2023-03-16 17:36:09,847] [INFO] DFAST_QC completed!
[2023-03-16 17:36:09,847] [INFO] Total running time: 0h1m8s