[2023-03-19 04:46:19,800] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:19,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:19,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference
[2023-03-19 04:46:20,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:20,892] [INFO] Task started: Prodigal
[2023-03-19 04:46:20,892] [INFO] Running command: cat /var/lib/cwl/stg5a2e5402-59da-44dd-a1ec-730c3cb47233/OceanDNA-a5076.fa | prodigal -d OceanDNA-a5076/cds.fna -a OceanDNA-a5076/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:26,870] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:26,870] [INFO] Task started: HMMsearch
[2023-03-19 04:46:26,870] [INFO] Running command: hmmsearch --tblout OceanDNA-a5076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference/reference_markers.hmm OceanDNA-a5076/protein.faa > /dev/null
[2023-03-19 04:46:27,025] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:27,026] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5a2e5402-59da-44dd-a1ec-730c3cb47233/OceanDNA-a5076.fa]
[2023-03-19 04:46:27,034] [INFO] Query marker FASTA was written to OceanDNA-a5076/markers.fasta
[2023-03-19 04:46:27,034] [INFO] Task started: Blastn
[2023-03-19 04:46:27,034] [INFO] Running command: blastn -query OceanDNA-a5076/markers.fasta -db /var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference/reference_markers.fasta -out OceanDNA-a5076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:27,455] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:27,456] [INFO] Selected 5 target genomes.
[2023-03-19 04:46:27,456] [INFO] Target genome list was writen to OceanDNA-a5076/target_genomes.txt
[2023-03-19 04:46:27,459] [INFO] Task started: fastANI
[2023-03-19 04:46:27,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a2e5402-59da-44dd-a1ec-730c3cb47233/OceanDNA-a5076.fa --refList OceanDNA-a5076/target_genomes.txt --output OceanDNA-a5076/fastani_result.tsv --threads 1
[2023-03-19 04:46:30,243] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:30,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:30,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:30,244] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:30,244] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:46:30,244] [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
--------------------------------------------------------------------------------
[2023-03-19 04:46:30,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5076/tc_result.tsv
[2023-03-19 04:46:30,245] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:30,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:30,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference/checkm_data
[2023-03-19 04:46:30,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:30,518] [INFO] Task started: CheckM
[2023-03-19 04:46:30,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5076/checkm_input OceanDNA-a5076/checkm_result
[2023-03-19 04:46:51,096] [INFO] Task succeeded: CheckM
[2023-03-19 04:46:51,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.23%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:46:51,099] [INFO] ===== Completeness check finished =====
[2023-03-19 04:46:51,099] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:46:51,099] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5076/markers.fasta)
[2023-03-19 04:46:51,099] [INFO] Task started: Blastn
[2023-03-19 04:46:51,099] [INFO] Running command: blastn -query OceanDNA-a5076/markers.fasta -db /var/lib/cwl/stg11d1048d-3ded-4cf2-9151-97639c5d23f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:51,515] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:51,516] [INFO] Selected 7 target genomes.
[2023-03-19 04:46:51,516] [INFO] Target genome list was writen to OceanDNA-a5076/target_genomes_gtdb.txt
[2023-03-19 04:46:51,524] [INFO] Task started: fastANI
[2023-03-19 04:46:51,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a2e5402-59da-44dd-a1ec-730c3cb47233/OceanDNA-a5076.fa --refList OceanDNA-a5076/target_genomes_gtdb.txt --output OceanDNA-a5076/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:46:53,245] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:53,250] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:46:53,250] [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_002505325.1	s__Thalassarchaeum sp002505325	99.2469	270	332	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002457605.1	s__Thalassarchaeum sp002457605	92.2132	238	332	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495735.1	s__Thalassarchaeum sp002495735	88.6215	245	332	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	88.3384	292	332	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	84.674	270	332	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002507125.1	s__Thalassarchaeum sp002507125	78.8944	129	332	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:46:53,250] [INFO] GTDB search result was written to OceanDNA-a5076/result_gtdb.tsv
[2023-03-19 04:46:53,250] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:46:53,251] [INFO] DFAST_QC result json was written to OceanDNA-a5076/dqc_result.json
[2023-03-19 04:46:53,251] [INFO] DFAST_QC completed!
[2023-03-19 04:46:53,251] [INFO] Total running time: 0h0m33s