[2023-03-15 08:59:48,851] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:48,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:48,852] [INFO] DQC Reference Directory: /var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference
[2023-03-15 08:59:49,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:49,988] [INFO] Task started: Prodigal
[2023-03-15 08:59:49,988] [INFO] Running command: cat /var/lib/cwl/stg19ec2ade-8d69-4675-93df-b284e2200224/OceanDNA-b36680.fa | prodigal -d OceanDNA-b36680/cds.fna -a OceanDNA-b36680/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:04,109] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:04,109] [INFO] Task started: HMMsearch
[2023-03-15 09:00:04,109] [INFO] Running command: hmmsearch --tblout OceanDNA-b36680/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference/reference_markers.hmm OceanDNA-b36680/protein.faa > /dev/null
[2023-03-15 09:00:04,318] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:04,319] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg19ec2ade-8d69-4675-93df-b284e2200224/OceanDNA-b36680.fa]
[2023-03-15 09:00:04,343] [INFO] Query marker FASTA was written to OceanDNA-b36680/markers.fasta
[2023-03-15 09:00:04,343] [INFO] Task started: Blastn
[2023-03-15 09:00:04,343] [INFO] Running command: blastn -query OceanDNA-b36680/markers.fasta -db /var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference/reference_markers.fasta -out OceanDNA-b36680/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:04,786] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:04,786] [INFO] Selected 23 target genomes.
[2023-03-15 09:00:04,787] [INFO] Target genome list was writen to OceanDNA-b36680/target_genomes.txt
[2023-03-15 09:00:04,800] [INFO] Task started: fastANI
[2023-03-15 09:00:04,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ec2ade-8d69-4675-93df-b284e2200224/OceanDNA-b36680.fa --refList OceanDNA-b36680/target_genomes.txt --output OceanDNA-b36680/fastani_result.tsv --threads 1
[2023-03-15 09:00:18,868] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:18,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:18,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:18,871] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:18,871] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:18,871] [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
Marinagarivorans algicola	strain=Z1	GCA_001292705.1	1513270	1513270	type	True	77.0132	88	793	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:18,871] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36680/tc_result.tsv
[2023-03-15 09:00:18,871] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:18,872] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:18,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference/checkm_data
[2023-03-15 09:00:18,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:18,878] [INFO] Task started: CheckM
[2023-03-15 09:00:18,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36680/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36680/checkm_input OceanDNA-b36680/checkm_result
[2023-03-15 09:00:57,665] [INFO] Task succeeded: CheckM
[2023-03-15 09:00:57,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:00:57,668] [INFO] ===== Completeness check finished =====
[2023-03-15 09:00:57,669] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:00:57,669] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36680/markers.fasta)
[2023-03-15 09:00:57,669] [INFO] Task started: Blastn
[2023-03-15 09:00:57,669] [INFO] Running command: blastn -query OceanDNA-b36680/markers.fasta -db /var/lib/cwl/stgceed20b7-c9df-458b-bd41-a5f81bc3308f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36680/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:58,098] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:58,099] [INFO] Selected 24 target genomes.
[2023-03-15 09:00:58,099] [INFO] Target genome list was writen to OceanDNA-b36680/target_genomes_gtdb.txt
[2023-03-15 09:00:58,128] [INFO] Task started: fastANI
[2023-03-15 09:00:58,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ec2ade-8d69-4675-93df-b284e2200224/OceanDNA-b36680.fa --refList OceanDNA-b36680/target_genomes_gtdb.txt --output OceanDNA-b36680/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:12,856] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:12,858] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:01:12,858] [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
GCF_001292705.1	s__Marinagarivorans algicola	77.0132	88	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinagarivorans	95.0	99.28	99.28	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:12,858] [INFO] GTDB search result was written to OceanDNA-b36680/result_gtdb.tsv
[2023-03-15 09:01:12,858] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:12,859] [INFO] DFAST_QC result json was written to OceanDNA-b36680/dqc_result.json
[2023-03-15 09:01:12,859] [INFO] DFAST_QC completed!
[2023-03-15 09:01:12,859] [INFO] Total running time: 0h1m24s