[2023-03-17 11:29:30,402] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:29:30,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:29:30,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference
[2023-03-17 11:29:31,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:29:31,512] [INFO] Task started: Prodigal
[2023-03-17 11:29:31,513] [INFO] Running command: cat /var/lib/cwl/stg628ad24d-d9a7-4c10-9ab7-ed6727371c8a/OceanDNA-a1624.fa | prodigal -d OceanDNA-a1624/cds.fna -a OceanDNA-a1624/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:29:35,471] [INFO] Task succeeded: Prodigal
[2023-03-17 11:29:35,471] [INFO] Task started: HMMsearch
[2023-03-17 11:29:35,471] [INFO] Running command: hmmsearch --tblout OceanDNA-a1624/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference/reference_markers.hmm OceanDNA-a1624/protein.faa > /dev/null
[2023-03-17 11:29:35,623] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:29:35,624] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg628ad24d-d9a7-4c10-9ab7-ed6727371c8a/OceanDNA-a1624.fa]
[2023-03-17 11:29:35,634] [INFO] Query marker FASTA was written to OceanDNA-a1624/markers.fasta
[2023-03-17 11:29:35,635] [INFO] Task started: Blastn
[2023-03-17 11:29:35,635] [INFO] Running command: blastn -query OceanDNA-a1624/markers.fasta -db /var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference/reference_markers.fasta -out OceanDNA-a1624/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:29:36,276] [INFO] Task succeeded: Blastn
[2023-03-17 11:29:36,276] [INFO] Selected 5 target genomes.
[2023-03-17 11:29:36,277] [INFO] Target genome list was writen to OceanDNA-a1624/target_genomes.txt
[2023-03-17 11:29:36,301] [INFO] Task started: fastANI
[2023-03-17 11:29:36,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg628ad24d-d9a7-4c10-9ab7-ed6727371c8a/OceanDNA-a1624.fa --refList OceanDNA-a1624/target_genomes.txt --output OceanDNA-a1624/fastani_result.tsv --threads 1
[2023-03-17 11:29:38,940] [INFO] Task succeeded: fastANI
[2023-03-17 11:29:38,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:29:38,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:29:38,941] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:29:38,941] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:29:38,941] [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 11:29:38,942] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1624/tc_result.tsv
[2023-03-17 11:29:38,942] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:29:38,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:29:38,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference/checkm_data
[2023-03-17 11:29:39,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:29:39,279] [INFO] Task started: CheckM
[2023-03-17 11:29:39,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1624/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1624/checkm_input OceanDNA-a1624/checkm_result
[2023-03-17 11:29:57,834] [INFO] Task succeeded: CheckM
[2023-03-17 11:29:57,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:29:57,849] [INFO] ===== Completeness check finished =====
[2023-03-17 11:29:57,849] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:29:57,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1624/markers.fasta)
[2023-03-17 11:29:57,851] [INFO] Task started: Blastn
[2023-03-17 11:29:57,851] [INFO] Running command: blastn -query OceanDNA-a1624/markers.fasta -db /var/lib/cwl/stg1827b47d-700f-4069-8e3b-8b401e825cf6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1624/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:29:58,597] [INFO] Task succeeded: Blastn
[2023-03-17 11:29:58,598] [INFO] Selected 10 target genomes.
[2023-03-17 11:29:58,598] [INFO] Target genome list was writen to OceanDNA-a1624/target_genomes_gtdb.txt
[2023-03-17 11:29:58,626] [INFO] Task started: fastANI
[2023-03-17 11:29:58,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg628ad24d-d9a7-4c10-9ab7-ed6727371c8a/OceanDNA-a1624.fa --refList OceanDNA-a1624/target_genomes_gtdb.txt --output OceanDNA-a1624/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:30:00,894] [INFO] Task succeeded: fastANI
[2023-03-17 11:30:00,896] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:30:00,897] [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_016845825.1	s__CG-Epi1 sp016845825	77.7472	54	206	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_001875345.1	s__CG-Epi1 sp001875345	77.4386	55	206	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 11:30:00,897] [INFO] GTDB search result was written to OceanDNA-a1624/result_gtdb.tsv
[2023-03-17 11:30:00,897] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:30:00,897] [INFO] DFAST_QC result json was written to OceanDNA-a1624/dqc_result.json
[2023-03-17 11:30:00,897] [INFO] DFAST_QC completed!
[2023-03-17 11:30:00,898] [INFO] Total running time: 0h0m30s