[2023-03-17 22:40:57,336] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:40:57,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:40:57,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference
[2023-03-17 22:40:58,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:40:58,416] [INFO] Task started: Prodigal
[2023-03-17 22:40:58,416] [INFO] Running command: cat /var/lib/cwl/stg91048e38-960e-4191-b776-041abc5fa769/OceanDNA-a4777.fa | prodigal -d OceanDNA-a4777/cds.fna -a OceanDNA-a4777/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:41:08,680] [INFO] Task succeeded: Prodigal
[2023-03-17 22:41:08,681] [INFO] Task started: HMMsearch
[2023-03-17 22:41:08,681] [INFO] Running command: hmmsearch --tblout OceanDNA-a4777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference/reference_markers.hmm OceanDNA-a4777/protein.faa > /dev/null
[2023-03-17 22:41:08,845] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:41:08,845] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg91048e38-960e-4191-b776-041abc5fa769/OceanDNA-a4777.fa]
[2023-03-17 22:41:08,859] [INFO] Query marker FASTA was written to OceanDNA-a4777/markers.fasta
[2023-03-17 22:41:08,860] [INFO] Task started: Blastn
[2023-03-17 22:41:08,860] [INFO] Running command: blastn -query OceanDNA-a4777/markers.fasta -db /var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference/reference_markers.fasta -out OceanDNA-a4777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:41:09,345] [INFO] Task succeeded: Blastn
[2023-03-17 22:41:09,345] [INFO] Selected 11 target genomes.
[2023-03-17 22:41:09,346] [INFO] Target genome list was writen to OceanDNA-a4777/target_genomes.txt
[2023-03-17 22:41:09,354] [INFO] Task started: fastANI
[2023-03-17 22:41:09,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg91048e38-960e-4191-b776-041abc5fa769/OceanDNA-a4777.fa --refList OceanDNA-a4777/target_genomes.txt --output OceanDNA-a4777/fastani_result.tsv --threads 1
[2023-03-17 22:41:14,871] [INFO] Task succeeded: fastANI
[2023-03-17 22:41:14,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:41:14,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:41:14,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:41:14,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:41:14,872] [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
--------------------------------------------------------------------------------
[2023-03-17 22:41:14,872] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4777/tc_result.tsv
[2023-03-17 22:41:14,873] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:41:14,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:41:14,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference/checkm_data
[2023-03-17 22:41:14,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:41:14,927] [INFO] Task started: CheckM
[2023-03-17 22:41:14,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4777/checkm_input OceanDNA-a4777/checkm_result
[2023-03-17 22:41:45,500] [INFO] Task succeeded: CheckM
[2023-03-17 22:41:45,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 1.30%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 22:41:45,503] [INFO] ===== Completeness check finished =====
[2023-03-17 22:41:45,504] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:41:45,504] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4777/markers.fasta)
[2023-03-17 22:41:45,504] [INFO] Task started: Blastn
[2023-03-17 22:41:45,504] [INFO] Running command: blastn -query OceanDNA-a4777/markers.fasta -db /var/lib/cwl/stg67e77fa2-4f6f-40b7-911d-461b5808379b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:41:46,147] [INFO] Task succeeded: Blastn
[2023-03-17 22:41:46,148] [INFO] Selected 9 target genomes.
[2023-03-17 22:41:46,148] [INFO] Target genome list was writen to OceanDNA-a4777/target_genomes_gtdb.txt
[2023-03-17 22:41:46,151] [INFO] Task started: fastANI
[2023-03-17 22:41:46,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg91048e38-960e-4191-b776-041abc5fa769/OceanDNA-a4777.fa --refList OceanDNA-a4777/target_genomes_gtdb.txt --output OceanDNA-a4777/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:41:48,500] [INFO] Task succeeded: fastANI
[2023-03-17 22:41:48,503] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:41:48,503] [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_002457195.1	s__MGIIb-P sp002457195	99.3655	344	523	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002498455.1	s__MGIIb-P sp002498455	77.4555	143	523	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	98.13	97.46	0.87	0.81	6	-
GCA_002505685.1	s__MGIIb-P sp002505685	77.411	129	523	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	99.68	99.68	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-17 22:41:48,504] [INFO] GTDB search result was written to OceanDNA-a4777/result_gtdb.tsv
[2023-03-17 22:41:48,504] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:41:48,505] [INFO] DFAST_QC result json was written to OceanDNA-a4777/dqc_result.json
[2023-03-17 22:41:48,505] [INFO] DFAST_QC completed!
[2023-03-17 22:41:48,505] [INFO] Total running time: 0h0m51s