[2023-03-15 23:15:05,777] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,777] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,778] [INFO] DQC Reference Directory: /var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference
[2023-03-15 23:15:07,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stg1a806559-0ac8-413b-8f22-12a6e66249b7/OceanDNA-a3708.fa | prodigal -d OceanDNA-a3708/cds.fna -a OceanDNA-a3708/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:14,438] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:14,438] [INFO] Task started: HMMsearch
[2023-03-15 23:15:14,438] [INFO] Running command: hmmsearch --tblout OceanDNA-a3708/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference/reference_markers.hmm OceanDNA-a3708/protein.faa > /dev/null
[2023-03-15 23:15:14,597] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:14,598] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1a806559-0ac8-413b-8f22-12a6e66249b7/OceanDNA-a3708.fa]
[2023-03-15 23:15:14,608] [INFO] Query marker FASTA was written to OceanDNA-a3708/markers.fasta
[2023-03-15 23:15:14,608] [INFO] Task started: Blastn
[2023-03-15 23:15:14,608] [INFO] Running command: blastn -query OceanDNA-a3708/markers.fasta -db /var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference/reference_markers.fasta -out OceanDNA-a3708/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:15,731] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:15,732] [INFO] Selected 5 target genomes.
[2023-03-15 23:15:15,732] [INFO] Target genome list was writen to OceanDNA-a3708/target_genomes.txt
[2023-03-15 23:15:15,737] [INFO] Task started: fastANI
[2023-03-15 23:15:15,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a806559-0ac8-413b-8f22-12a6e66249b7/OceanDNA-a3708.fa --refList OceanDNA-a3708/target_genomes.txt --output OceanDNA-a3708/fastani_result.tsv --threads 1
[2023-03-15 23:15:18,147] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:18,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:18,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:18,148] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:18,148] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:15:18,148] [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
--------------------------------------------------------------------------------
[2023-03-15 23:15:18,149] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3708/tc_result.tsv
[2023-03-15 23:15:18,149] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:18,149] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:18,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference/checkm_data
[2023-03-15 23:15:18,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:18,157] [INFO] Task started: CheckM
[2023-03-15 23:15:18,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3708/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3708/checkm_input OceanDNA-a3708/checkm_result
[2023-03-15 23:15:40,832] [INFO] Task succeeded: CheckM
[2023-03-15 23:15:40,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:15:40,871] [INFO] ===== Completeness check finished =====
[2023-03-15 23:15:40,872] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:15:40,872] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3708/markers.fasta)
[2023-03-15 23:15:40,873] [INFO] Task started: Blastn
[2023-03-15 23:15:40,873] [INFO] Running command: blastn -query OceanDNA-a3708/markers.fasta -db /var/lib/cwl/stgdefd6cc7-abb3-40ce-ac45-27771678e1ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3708/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:41,415] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:41,418] [INFO] Selected 7 target genomes.
[2023-03-15 23:15:41,418] [INFO] Target genome list was writen to OceanDNA-a3708/target_genomes_gtdb.txt
[2023-03-15 23:15:41,426] [INFO] Task started: fastANI
[2023-03-15 23:15:41,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a806559-0ac8-413b-8f22-12a6e66249b7/OceanDNA-a3708.fa --refList OceanDNA-a3708/target_genomes_gtdb.txt --output OceanDNA-a3708/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:15:43,367] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:43,373] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:15:43,373] [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_016777225.1	s__MGIIb-O2 sp016777225	80.6296	301	426	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_002494975.1	s__MGIIb-O2 sp002494975	79.9135	236	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.81	97.76	0.81	0.69	24	-
GCA_902514485.1	s__MGIIb-O2 sp902514485	79.4602	158	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	98.21	0.74	0.74	2	-
GCA_002497245.1	s__MGIIb-O2 sp002497245	77.9926	179	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	-
GCA_002504905.1	s__MGIIb-O2 sp002504905	77.836	191	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
GCA_902593945.1	s__MGIIb-O2 sp902593945	77.7773	159	426	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_002495525.1	s__MGIIb-O2 sp002495525	77.7729	177	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	96.68	0.79	0.75	3	-
--------------------------------------------------------------------------------
[2023-03-15 23:15:43,374] [INFO] GTDB search result was written to OceanDNA-a3708/result_gtdb.tsv
[2023-03-15 23:15:43,376] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:15:43,377] [INFO] DFAST_QC result json was written to OceanDNA-a3708/dqc_result.json
[2023-03-15 23:15:43,377] [INFO] DFAST_QC completed!
[2023-03-15 23:15:43,377] [INFO] Total running time: 0h0m38s