[2023-03-16 07:28:29,973] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference
[2023-03-16 07:28:31,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,096] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,096] [INFO] Running command: cat /var/lib/cwl/stg78edfb9c-873b-44be-9ba8-5fcb491eebe2/OceanDNA-a4358.fa | prodigal -d OceanDNA-a4358/cds.fna -a OceanDNA-a4358/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:39,406] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:39,407] [INFO] Task started: HMMsearch
[2023-03-16 07:28:39,407] [INFO] Running command: hmmsearch --tblout OceanDNA-a4358/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference/reference_markers.hmm OceanDNA-a4358/protein.faa > /dev/null
[2023-03-16 07:28:39,556] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:39,556] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg78edfb9c-873b-44be-9ba8-5fcb491eebe2/OceanDNA-a4358.fa]
[2023-03-16 07:28:39,569] [INFO] Query marker FASTA was written to OceanDNA-a4358/markers.fasta
[2023-03-16 07:28:39,571] [INFO] Task started: Blastn
[2023-03-16 07:28:39,571] [INFO] Running command: blastn -query OceanDNA-a4358/markers.fasta -db /var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference/reference_markers.fasta -out OceanDNA-a4358/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:39,998] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:40,000] [INFO] Selected 4 target genomes.
[2023-03-16 07:28:40,000] [INFO] Target genome list was writen to OceanDNA-a4358/target_genomes.txt
[2023-03-16 07:28:40,004] [INFO] Task started: fastANI
[2023-03-16 07:28:40,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg78edfb9c-873b-44be-9ba8-5fcb491eebe2/OceanDNA-a4358.fa --refList OceanDNA-a4358/target_genomes.txt --output OceanDNA-a4358/fastani_result.tsv --threads 1
[2023-03-16 07:28:41,651] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:41,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:41,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:41,652] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:41,652] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:28:41,652] [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 07:28:41,653] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4358/tc_result.tsv
[2023-03-16 07:28:41,654] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:41,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:41,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference/checkm_data
[2023-03-16 07:28:41,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:41,819] [INFO] Task started: CheckM
[2023-03-16 07:28:41,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4358/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4358/checkm_input OceanDNA-a4358/checkm_result
[2023-03-16 07:29:07,593] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:07,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:07,595] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:07,595] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:07,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4358/markers.fasta)
[2023-03-16 07:29:07,596] [INFO] Task started: Blastn
[2023-03-16 07:29:07,596] [INFO] Running command: blastn -query OceanDNA-a4358/markers.fasta -db /var/lib/cwl/stg9d70c1bd-9af0-4b43-8e7b-e9ec3c957b9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4358/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:08,026] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:08,027] [INFO] Selected 9 target genomes.
[2023-03-16 07:29:08,027] [INFO] Target genome list was writen to OceanDNA-a4358/target_genomes_gtdb.txt
[2023-03-16 07:29:08,163] [INFO] Task started: fastANI
[2023-03-16 07:29:08,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg78edfb9c-873b-44be-9ba8-5fcb491eebe2/OceanDNA-a4358.fa --refList OceanDNA-a4358/target_genomes_gtdb.txt --output OceanDNA-a4358/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:10,384] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:10,388] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:29:10,388] [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_002503285.1	s__MGIIb-O3 sp002503285	99.8578	484	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.00	95.68	0.94	0.92	11	conclusive
GCA_016777225.1	s__MGIIb-O2 sp016777225	77.6631	77	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172375.1	s__MGIIb-O3 sp002172375	77.264	112	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731195.1	s__MGIIb-O3 sp002731195	77.2012	111	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:10,388] [INFO] GTDB search result was written to OceanDNA-a4358/result_gtdb.tsv
[2023-03-16 07:29:10,388] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:10,389] [INFO] DFAST_QC result json was written to OceanDNA-a4358/dqc_result.json
[2023-03-16 07:29:10,389] [INFO] DFAST_QC completed!
[2023-03-16 07:29:10,389] [INFO] Total running time: 0h0m40s