[2023-03-18 01:54:19,368] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:19,368] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:19,368] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference
[2023-03-18 01:54:20,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:20,483] [INFO] Task started: Prodigal
[2023-03-18 01:54:20,483] [INFO] Running command: cat /var/lib/cwl/stg1d2dd176-ce76-438b-a558-8a85cd026cae/OceanDNA-b12070.fa | prodigal -d OceanDNA-b12070/cds.fna -a OceanDNA-b12070/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:28,955] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:28,955] [INFO] Task started: HMMsearch
[2023-03-18 01:54:28,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b12070/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference/reference_markers.hmm OceanDNA-b12070/protein.faa > /dev/null
[2023-03-18 01:54:29,115] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:29,115] [INFO] Found 6/6 markers.
[2023-03-18 01:54:29,152] [INFO] Query marker FASTA was written to OceanDNA-b12070/markers.fasta
[2023-03-18 01:54:29,153] [INFO] Task started: Blastn
[2023-03-18 01:54:29,153] [INFO] Running command: blastn -query OceanDNA-b12070/markers.fasta -db /var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference/reference_markers.fasta -out OceanDNA-b12070/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:29,676] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:29,677] [INFO] Selected 32 target genomes.
[2023-03-18 01:54:29,677] [INFO] Target genome list was writen to OceanDNA-b12070/target_genomes.txt
[2023-03-18 01:54:29,696] [INFO] Task started: fastANI
[2023-03-18 01:54:29,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d2dd176-ce76-438b-a558-8a85cd026cae/OceanDNA-b12070.fa --refList OceanDNA-b12070/target_genomes.txt --output OceanDNA-b12070/fastani_result.tsv --threads 1
[2023-03-18 01:54:46,845] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:46,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:46,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:46,846] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:46,846] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:54:46,846] [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
--------------------------------------------------------------------------------
[2023-03-18 01:54:46,868] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12070/tc_result.tsv
[2023-03-18 01:54:46,868] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:46,868] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:46,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference/checkm_data
[2023-03-18 01:54:46,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:46,876] [INFO] Task started: CheckM
[2023-03-18 01:54:46,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12070/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12070/checkm_input OceanDNA-b12070/checkm_result
[2023-03-18 01:55:13,484] [INFO] Task succeeded: CheckM
[2023-03-18 01:55:13,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:55:13,555] [INFO] ===== Completeness check finished =====
[2023-03-18 01:55:13,555] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:55:13,555] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12070/markers.fasta)
[2023-03-18 01:55:13,556] [INFO] Task started: Blastn
[2023-03-18 01:55:13,556] [INFO] Running command: blastn -query OceanDNA-b12070/markers.fasta -db /var/lib/cwl/stgf2a20623-79bb-42f6-8d06-bb5922a089a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12070/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:55:14,255] [INFO] Task succeeded: Blastn
[2023-03-18 01:55:14,259] [INFO] Selected 25 target genomes.
[2023-03-18 01:55:14,259] [INFO] Target genome list was writen to OceanDNA-b12070/target_genomes_gtdb.txt
[2023-03-18 01:55:14,314] [INFO] Task started: fastANI
[2023-03-18 01:55:14,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d2dd176-ce76-438b-a558-8a85cd026cae/OceanDNA-b12070.fa --refList OceanDNA-b12070/target_genomes_gtdb.txt --output OceanDNA-b12070/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:55:25,208] [INFO] Task succeeded: fastANI
[2023-03-18 01:55:25,212] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:55:25,212] [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	98.2877	203	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	98.75	98.75	0.58	0.58	2	conclusive
GCA_002723115.1	s__UBA974 sp002723115	79.3016	161	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722795.1	s__UBA974 sp002722795	78.7367	180	403	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	77.9218	134	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:55:25,212] [INFO] GTDB search result was written to OceanDNA-b12070/result_gtdb.tsv
[2023-03-18 01:55:25,227] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:55:25,232] [INFO] DFAST_QC result json was written to OceanDNA-b12070/dqc_result.json
[2023-03-18 01:55:25,232] [INFO] DFAST_QC completed!
[2023-03-18 01:55:25,232] [INFO] Total running time: 0h1m6s