[2023-03-17 04:15:14,715] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference
[2023-03-17 04:15:16,098] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,098] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,098] [INFO] Running command: cat /var/lib/cwl/stgd86dad4d-d7ee-433b-9c24-84190790e867/OceanDNA-a1565.fa | prodigal -d OceanDNA-a1565/cds.fna -a OceanDNA-a1565/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:20,738] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:20,738] [INFO] Task started: HMMsearch
[2023-03-17 04:15:20,739] [INFO] Running command: hmmsearch --tblout OceanDNA-a1565/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference/reference_markers.hmm OceanDNA-a1565/protein.faa > /dev/null
[2023-03-17 04:15:21,089] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:21,089] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd86dad4d-d7ee-433b-9c24-84190790e867/OceanDNA-a1565.fa]
[2023-03-17 04:15:21,097] [INFO] Query marker FASTA was written to OceanDNA-a1565/markers.fasta
[2023-03-17 04:15:21,109] [INFO] Task started: Blastn
[2023-03-17 04:15:21,109] [INFO] Running command: blastn -query OceanDNA-a1565/markers.fasta -db /var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference/reference_markers.fasta -out OceanDNA-a1565/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:21,795] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:21,796] [INFO] Selected 5 target genomes.
[2023-03-17 04:15:21,796] [INFO] Target genome list was writen to OceanDNA-a1565/target_genomes.txt
[2023-03-17 04:15:21,799] [INFO] Task started: fastANI
[2023-03-17 04:15:21,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgd86dad4d-d7ee-433b-9c24-84190790e867/OceanDNA-a1565.fa --refList OceanDNA-a1565/target_genomes.txt --output OceanDNA-a1565/fastani_result.tsv --threads 1
[2023-03-17 04:15:24,129] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:24,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:24,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:24,130] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:24,130] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:15:24,130] [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 04:15:24,130] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1565/tc_result.tsv
[2023-03-17 04:15:24,131] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:24,131] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:24,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference/checkm_data
[2023-03-17 04:15:24,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:24,184] [INFO] Task started: CheckM
[2023-03-17 04:15:24,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1565/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1565/checkm_input OceanDNA-a1565/checkm_result
[2023-03-17 04:15:46,500] [INFO] Task succeeded: CheckM
[2023-03-17 04:15:46,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:15:46,502] [INFO] ===== Completeness check finished =====
[2023-03-17 04:15:46,502] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:15:46,503] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1565/markers.fasta)
[2023-03-17 04:15:46,505] [INFO] Task started: Blastn
[2023-03-17 04:15:46,505] [INFO] Running command: blastn -query OceanDNA-a1565/markers.fasta -db /var/lib/cwl/stg5640ab69-16e9-46af-b293-50e28ebdf2b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1565/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:47,334] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:47,334] [INFO] Selected 5 target genomes.
[2023-03-17 04:15:47,334] [INFO] Target genome list was writen to OceanDNA-a1565/target_genomes_gtdb.txt
[2023-03-17 04:15:47,545] [INFO] Task started: fastANI
[2023-03-17 04:15:47,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgd86dad4d-d7ee-433b-9c24-84190790e867/OceanDNA-a1565.fa --refList OceanDNA-a1565/target_genomes_gtdb.txt --output OceanDNA-a1565/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:15:48,676] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:48,679] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:15:48,679] [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_014240255.1	s__CG-Epi1 sp014240255	88.4081	231	274	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240055.1	s__CG-Epi1 sp014240055	83.8919	215	274	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	77.6706	67	274	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:15:48,679] [INFO] GTDB search result was written to OceanDNA-a1565/result_gtdb.tsv
[2023-03-17 04:15:48,679] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:15:48,680] [INFO] DFAST_QC result json was written to OceanDNA-a1565/dqc_result.json
[2023-03-17 04:15:48,680] [INFO] DFAST_QC completed!
[2023-03-17 04:15:48,680] [INFO] Total running time: 0h0m34s